arXiv subjects

Michael Bachmann

Publications and source records attributed to Michael Bachmann.

At least 55 records · Page 3Linked to original sources

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↗

arXiv2011

Spin caloritronics in magnetic tunnel junctions: Ab initio studies

This Letter presents ab initio calculations of the magneto-thermoelectric power (MTEP) and of the spin-Seebeck coefficient in MgO based tunnel junctions with Fe and Co leads. In addition, the normal thermopower is calculated and gives for pure Fe and Co an quantitative agreement with experiments. Consequently, the calculated values in tunnel junctions are a good estimation of upper limits. In particular, spin-Seebeck coefficients of more than 100 μV/K are possible. The MTEP ratio exceed several 1000% and depends strongly on temperature. In the case of Fe leads the MTEP ratio diverges even to infinity at certain temperatures. The spin-Seebeck coefficient as a function of temperature shows a non-trivial dependence. For Fe/MgO/Fe even the sign of the coefficient changes with temperature.

cond-mat.mes-hall↗

arXiv2011

Accurate modeling approach for the structural comparison between monolayer polymer tubes and single-walled nanotubes

In a recent computational study, we found highly structured ground states for coarse-grained polymers adsorbed to ultrathin nanowires in a certain model parameter region. Those tubelike configurations show, even at a first glance, exciting morphological similarities to known atomistic nanotubes such as single-walled carbon nanotubes. In order to explain those similarities in a systematic way, we performed additional detailed and extensive simulations of coarse-grained polymer models with various parameter settings. We show this here and explain why standard geometrical models for atomistic nanotubes are not suited to interpret the results of those studies. In fact, the general structural behavior of polymer nanotubes, as well as specific previous observations, can only be explained by applying recently developed polyhedral tube models.

cond-mat.soft↗

arXiv2011

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.

cond-mat.soft↗

arXiv2011

Structural Arrangements of Polymers Adsorbed at Nanostrings

We study ground states of a hybrid system consisting of a polymer and an attractive nanowire by means of 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 construct the complete conformational phase diagram and analyze in more detail particularly interesting polymer-tube conformations.

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↗

arXiv2010

Surface effects in the crystallization process of elastic flexible polymers

Investigating thermodynamic properties of liquid-solid transitions of flexible homopolymers with elastic bonds by means of multicanonical Monte Carlo simulations, we find crystalline conformations that resemble ground-state structures of Lennard-Jones clusters. This allows us to set up a structural classification scheme for finite-length flexible polymers and their freezing mechanism in analogy to atomic cluster formation. Crystals of polymers with "magic length" turn out to be perfectly icosahedral.

cond-mat.soft↗

arXiv2010

Ground-state properties of tubelike flexible polymers

In this work we investigate structural properties of native states of a simple model for short flexible homopolymers, where the steric influence of monomeric side chains is effectively introduced by a thickness constraint. This geometric constraint is implemented through the concept of the global radius of curvature and affects the conformational topology of ground-state structures. A systematic analysis allows for a thickness-dependent classification of the dominant ground-state topologies. It turns out that helical structures, strands, rings, and coils are natural, intrinsic geometries of such tubelike objects.

cond-mat.soft↗

arXiv2010

Systematic Microcanonical Analyses of Polymer Adsorption Transitions

In detailed microcanonical analyses of densities of states obtained by extensive multicanonical Monte Carlo computer simulations, we investigate the caloric properties of conformational transitions adsorbing polymers experience near attractive substrates. For short chains and strong surface attraction, the microcanonical entropy turns out to be a convex function of energy in the transition regime, indicating that surface-entropic effects are relevant. Albeit known to be a continuous transition in the thermodynamic limit of infinitely long chains, the adsorption transition of nongrafted finite-length polymers thus exhibits a clear signature of a first-order-like transition, with coexisting phases of adsorbed and desorbed conformations. Another remarkable consequence of the convexity of the microcanonical entropy is that the transition is accompanied by a decrease of the microcanonical temperature with increasing energy. Since this is a characteristic physical effect it might not be ignored in analyses of cooperative macrostate transitions in finite systems.

cond-mat.stat-mech↗

arXiv2010

Conformational phase diagram for polymers adsorbed at ultrathin nanowires

We study the conformational behavior of a polymer adsorbed at an attractive nanostring and construct the complete structural phase diagram in dependence of the binding strength and effective thickness of the string. For this purpose, Monte Carlo optimization techniques are employed to identify lowest-energy structures for a coarse-grained hybrid polymer-wire model. Among the representative conformations in the different phases are, for example, compact droplets attached to the string and also nanotube-like monolayer films wrapping the string in a very ordered way. We here systematically analyze low-energy shapes and structural order parameters to elucidate the transitions between the structural phases.

cond-mat.soft↗

arXiv2009

Conformational Mechanics of Polymer Adsorption Transitions at Attractive Substrates

Conformational phases of a semiflexible off-lattice homopolymer model near an attractive substrate are investigated by means of multicanonical computer simulations. In our polymer-substrate model, nonbonded pairs of monomers as well as monomers and the substrate interact via attractive van der Waals forces. To characterize conformational phases of this hybrid system, we analyze thermal fluctuations of energetic and structural quantities, as well as adequate docking parameters. Introducing a solvent parameter related to the strength of the surface attraction, we construct and discuss the solubility-temperature phase diagram. Apart from the main phases of adsorbed and desorbed conformations, we identify several other phase transitions such as the freezing transition between energy-dominated crystalline low-temperature structures and globular entropy-dominated conformations.

physics.comp-ph↗

arXiv2009

Thermodynamics of tubelike flexible polymers

In this work we present the general phase behavior of short tubelike flexible polymers. The geometric thickness constraint is implemented through the concept of the global radius of curvature. We use sophisticated Monte Carlo sampling methods to simulate small bead-stick polymer models with Lennard-Jones interaction among non-bonded monomers. We analyze energetic fluctuations and structural quantities to classify conformational pseudophases. We find that the tube thickness influences the thermodynamic behavior of simple tubelike polymers significantly, i.e., for given temperature, the formation of secondary structures strongly depends on the tube thickness.

cond-mat.soft↗

arXiv2009

Conformational Transitions in Molecular Systems

Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

cond-mat.stat-mech↗

arXiv2009

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.

cond-mat.soft↗

arXiv2009

Freezing and collapse of flexible polymers

We analyze the freezing 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↗

arXiv2009

Comparative Molecular Dynamics and Monte Carlo Study of Statistical Properties for Coarse-Grained Heteropolymers

Employing a simple hydrophobic-polar heteropolymer model, we compare thermodynamic quantities obtained from Andersen and Nose-Hoover molecular dynamics as well as replica-exchange Monte Carlo methods. We find qualitative correspondence in the results, but serious quantitative differences using the Nose-Hoover chain thermostat. For analyzing the deviations, we study different parameterizations of the Nose-Hoover chain thermostat. Autocorrelations from molecular dynamics and Metropolis Monte Carlo runs are also investigated.

cond-mat.stat-mech↗

arXiv2009

Mesoscopic Properties of Molecular Folding and Aggregation Processes

Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative behavior of the molecular subunits lining up to build chainlike macromolecules. Proteins experience conformational transitions related to thermodynamic phase transitions. For chains of finite length, an important difference of crossovers between conformational (pseudo)phases is, however, that these transitions are typically rather smooth processes, i.e., thermodynamic activity is not necessarily signalized by strong entropic or energetic fluctuations. Nonetheless, in order to understand generic properties of molecular structure-formation processes, the analysis of mesoscopic models from a statistical physics point of view enables first insights into the nature of conformational transitions in small systems. Here, we review recent results obtained by means of sophisticated generalized-ensemble computer simulations of minimalistic coarse-grained models.

cond-mat.stat-mech↗

arXiv2009

Thickness-dependent secondary structure formation of tubelike polymers

By means of sophisticated Monte Carlo methods, we investigate the conformational phase diagram of a simple model for flexible polymers with explicit thickness. The thickness constraint, which is introduced geometrically via the global radius of curvature of a polymer conformation, accounts for the excluded volume of the polymer and induces cooperative effects supporting the formation of secondary structures. In our detailed analysis of the temperature and thickness dependence of the conformational behavior for classes of short tubelike polymers, we find that known secondary-structure segments like helices and turns, but also ringlike conformations and stiff rods are dominant intrinsic topologies governing the phase behavior of such cooperative tubelike objects. This shows that the thickness constraint is indeed a fundamental physical parameter that allows for a classification of generic polymer structures.

cond-mat.soft↗