arXiv subjects

Michael Bachmann

Publications and source records attributed to Michael Bachmann.

84 records · Page 5Linked to original sources

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↗

arXiv2005

Conformational Transitions of Non-Grafted Polymers Near an Adsorbing Substrate

We have performed multicanonical chain-growth simulations of a polymer interacting with an adsorbing surface. The polymer, which is not explicitly anchored at the surface, experiences a hierarchy of phase transitions between conformations binding and non-binding with the substrate. We discuss the phase diagram in the temperature-solubility plane and highlight the transition ``path'' through the free-energy landscape.

cond-mat.stat-mech↗

arXiv2005

Exact Enumeration of Three-Dimensional Lattice Proteins

We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing sequences of HP proteins consisting of up to 19 monomers whose conformations are represented by interacting self-avoiding walks on the simple cubic lattice. Employing a parallelized implementation on a Linux cluster, we generate the complete set of contact maps of such walks.

cond-mat.stat-mech↗

arXiv2005

Multicanonical Study of Coarse-Grained Off-Lattice Models for Folding Heteropolymers

We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions of selected sequences with 20 monomers. Another aspect of the investigation was the comparison with the purely hydrophobic homopolymer and the study of general conformational properties induced by the "disorder" in the sequence of a heteropolymer. Furthermore, we applied an optimization algorithm to sequences with up to 55 monomers and compared the global-energy minimum found with lowest-energy states identified within the multicanonical simulation. This was used to find out how reliable the multicanonical method samples the free-energy landscape, in particular for low temperatures.

cond-mat.stat-mech↗

arXiv2004

Exact Sequence Analysis for Three-Dimensional HP Lattice Proteins

We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a non-degenerate ground state. Furthermore we were interested in characteristic thermodynamic properties of HP proteins with designing sequences. In order to be able to perform these exact studies, we applied an efficient enumeration method based on contact sets.

q-bio.BM↗

arXiv2003

Thermodynamics of Lattice Heteropolymers

We calculate thermodynamic quantities of HP lattice proteins by means of a multicanonical chain growth algorithm that connects the new variants of the Pruned-Enriched Rosenbluth Method (nPERM) and flat histogram sampling of the entire energy space. Since our method directly simulates the density of states, we obtain results for thermodynamic quantities of the system for all temperatures. In particular, this algorithm enables us to accurately simulate the usually difficult accessible low-temperature region. Therefore, it becomes possible to perform detailed analyses of the low-temperature transition between ground states and compact globules.

cond-mat.soft↗

arXiv2003

Multicanonical Chain Growth Algorithm

We present a temperature-independent Monte Carlo method for the determination of the density of states of lattice proteins that combines the fast ground-state search strategy of the nPERM chain growth and multicanonical reweighting for sampling the complete energy space. Since the density of states contains all energetic information of a statistical system, we can directly calculate the mean energy, specific heat, Gibbs free energy, and entropy for all temperatures. We apply this method to HP lattice proteins and for the examples of sequences considered, we identify the transitions between native, globule, and random coil states. Since no special properties of heteropolymers are involved in this algorithm, the method applies to polymer models as well.

cond-mat.stat-mech↗

arXiv2001

Functional Closure of Schwinger-Dyson Equations in Quantum Electrodynamics, Part 1: Generation of Connected and One-Particle Irreducible Feynman Diagrams

Using functional derivatives with respect to free propagators and interactions we derive a closed set of Schwinger-Dyson equations in quantum electrodynamics. Its conversion to graphical recursion relations allows us to systematically generate all connected and one-particle irreducible Feynman diagrams for the $n$-point functions and the vacuum energy together with their correct weights.

hep-th↗

arXiv2000

Fluctuation Pressure of a Stack of Membranes

We calculate the universal pressure constants of a stack of N membranes between walls by strong-coupling theory. The results are in very good agreement with values from Monte-Carlo simulations.

cond-mat↗

arXiv2000

Quantum Statistics of Hydrogen in Strong Magnetic Fields

By an extension of the Feynman-Kleinert variational approach, we calculate the temperature-dependent effective classical potential governing the quantum statistical properties of a hydrogen atom in a uniform magnetic field. In the zero-temperature limit, we obtain ground state energies which are accurate for all magnetic field strengths from weak to strong fields.

quant-ph↗

arXiv1999

Period-doubling bifurcation in strongly anisotropic Bianchi I quantum cosmology

We solve the Wheeler-DeWitt equation for the minisuperspace of a cosmological model of Bianchi type I with a minimally coupled massive scalar field $ϕ$ as source by generalizing the calculation of Lukash and Schmidt [1]. Contrarily to other approaches we allow strong anisotropy. Combining analytical and numerical methods, we apply an adiabatic approximation for $ϕ$, and as new feature we find a period-doubling bifurcation. This bifurcation takes place near the cosmological quantum boundary, i.e., the boundary of the quasiclassical region with oscillating $ψ$-function where the WKB-approximation is good. The numerical calculations suggest that such a notion of a ``cosmological quantum boundary'' is well-defined, because sharply beyond that boundary, the WKB-approximation is no more applicable at all. This result confirms the adequateness of the introduction of a cosmological quantum boundary in quantum cosmology.

gr-qc↗

arXiv1999

Generating Functionals for Harmonic Expectation Values of Paths with Fixed End Points. Feynman Diagrams for Nonpolynomial Interactions

We introduce a general class of generating functionals for the calculation of quantum-mechanical expectation values of arbitrary functionals of fluctuating paths with fixed end points in configuration or momentum space. The generating functionals are calculated explicitly for harmonic oscillators with time-dependent frequency, and used to derive a smearing formulas for correlation functions of polynomial and nonpolynomials functions of time-dependent positions and momenta. These formulas summarize the effect of thermal and quantum fluctuations, and serve to derive generalized Wick rules and Feynman diagrams for perturbation expansions of nonpolynomial interactions.

quant-ph↗