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.Comment: 10 pages, 11 figure

Different Kinds of Protein Folding Identified with a Coarse-Grained Heteropolymer Model

Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing the equilibrium conformations with the folded state in terms of an angular overlap parameter. Although all investigated heteropolymer sequences contain the same content of hydrophobic and polar monomers, our analysis of the folding channels reveals a variety of characteristic folding behaviors known from realistic peptides.Comment: 3 pages, 2 figure

Identification of Characteristic Protein Folding Channels in a Coarse-Grained Hydrophobic-Polar Peptide Model

Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a heteropolymer sequence lead to completely different folding behaviors. Studying three exemplified sequences with the same content of hydrophobic and polar residues, we can reproduce within this simple model two-state folding, folding through intermediates, as well as metastability.Comment: 26 pages, 6 figure

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.Comment: 9 pages, 17 figure

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.Comment: 10 pages, 1 figur

Adsorption of polymers at nanowires

Low-energy structures of a hybrid system consisting of a polymer and an attractive nanowire substrate as well as the thermodynamics of the adsorption transition are studied by means of Monte Carlo computer simulations. Depending on structural and energetic properties of the substrate, we find different adsorbed polymer conformations, amongst which are spherical droplets attached to the wire and monolayer tubes surrounding it. We identify adsorption temperatures and the type of the transition between adsorbed and desorbed structures depending on the substrate attraction strength.Comment: Proceedings of the Computational Physics Conference CCP 2010, Jun 23-27, 2010, Trondheim, Norwa

Vehicle to Everything Communication using VLC

Autonomous vehicles are currently self contained. However, we are coming to an age where there will be so many smart vehicles on the road, they will need a way to communicate with each other. In addition, the radio frequency spectrum is crowded and additional communication methods are needed to keep up with future needs. With these two ideas, this paper looks into a very new and developing form of communication - visible light communication - to provide an alternative to traditional radio waves for vehicular communication. We analyze the viability of this system as a proof-of-concept for the technology. We also present a design-prototype of a VLC vehicular transmitter and receiver to establish a wireless communication channel. We hope that our work can help provide a foundation for such a system being used in vehicles in a connected network