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Search Results: 1 - 10 of 45090 matches for " Michael Bachmann "
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Monte Carlo Simulations
Michael Bachmann
Physics , 2011,
Abstract: Monte Carlo computer simulations are virtually the only way to analyze the thermodynamic behavior of a system in a precise way. However, the various existing methods exhibit extreme differences in their efficiency, depending on model details and relevant questions. The original standard method, Metropolis Monte Carlo, which provides only reliable statistical information at a given (not too low) temperature has meanwhile been replaced by more sophisticated methods which are typically far more efficient (the differences in time scales can be compared with the age of the universe). However, none of the methods yields automatically accurate results, i.e., a system-specific adaptation and control is always needed. Thus, as in any good experiment, the most important part of the data analysis is statistical error estimation.
Effective Classical Hamiltonian from Perturbatively Defined Path Integral
Michael Bachmann
Physics , 2011,
Abstract: Introducing a perturbative definition, phase space path integrals can be calculated without slicing. This leads to a short-time expansion of the quantum-mechanical path amplitude, or a high-temperature expansion of the unnormalized density matrix, respectively. We use the proposed formalism to calculate the effective classical Hamiltonian for the harmonic oscillator.
Contact-Density Analysis of Lattice Polymer Adsorption Transitions
Michael Bachmann
Quantitative Biology , 2011,
Abstract: By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and monomer-monomer contacts. These contact numbers represent natural order parameters and allow for a comprising statistical study of the conformational space accessible to the polymer in dependence of external parameters such as the attraction strength of the substrate and the temperature. Since the contact density is independent of the energy scales associated to the interactions, its logarithm is an unbiased measure for the entropy of the conformational space. By setting explicit energy scales, the thus defined, highly general microcontact entropy can easily be related to the microcanonical entropy of the corresponding hybrid polymer-substrate system.
Statistical Analysis of Structural Transitions in Small Systems
Michael Bachmann
Quantitative Biology , 2011,
Abstract: We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to thermodynamic phase transitions, but also significant differences as the systems that we investigate here are very small. The usefulness of a microcanonical statistical analysis of these transitions in comparison with a canonical interpretation is emphasized. The results are obtained by employing sophisticated generalized-ensemble Markov-chain Monte Carlo methodologies.
Conformational phase diagram for polymers adsorbed at ultrathin nanowires
Thomas Vogel,Michael Bachmann
Physics , 2010, DOI: 10.1103/PhysRevLett.104.198302
Abstract: 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.
Mesoscopic Properties of Molecular Folding and Aggregation Processes
Michael Bachmann,Wolfhard Janke
Physics , 2009,
Abstract: 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.
Reduction to the Simplest - The Complexity of Minimalistic Heteropolymer Models
Michael Bachmann,Wolfhard Janke
Physics , 2007,
Abstract: 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.
Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives
Michael Bachmann,Wolfhard Janke
Physics , 2007,
Abstract: Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and function of complex macromolecules. This is reasoned by the interdisciplinary character of the associated questions ranging from the molecular origin of the loss of biological functionality as, for example, in Alzheimer's disease to the development of organic circuits for biosensory applications. In this lecture, we focus on the analysis of mesoscopic models for protein folding, aggregation, and hybrid systems of soft and solid condensed matter. The simplicity of the coarse-grained models allows for a more universal description of the notoriously difficult problem of protein folding. In this approach, classifications of structure formation processes with respect to the conformational pseudophases are possible. This is similar in aggregation and adsorption processes, where the individual folding propensity is influenced by external forces. The main problem in studies of conformational transitions is that the sequences of amino acids proteins are built up of are necessarily of finite length and, therefore, a thermodynamic limit does not exist. Thus, structural transitions are not phase transitions in the strict thermodynamic sense and the analysis of pseudouniversal aspects is intricate, as apparently small-system effects accompany all conformational transitions and cannot be neglected.
Adsorption Phenomena at Organic-Inorganic Interfaces
Michael Bachmann,Wolfhard Janke
Physics , 2007,
Abstract: 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.
Substrate Specificity of Peptide Adsorption: A Model Study
Michael Bachmann,Wolfhard Janke
Physics , 2007, DOI: 10.1103/PhysRevE.73.020901
Abstract: 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.
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