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Ulrich H. E. Hansmann

Publications and source records attributed to Ulrich H. E. Hansmann.

At least 37 records · Page 2Linked to original sources
arXiv2000

Is there a universality of the helix-coil transition in protein models?

The similarity in the thermodynamic properties of two completely different theoretical models for the helix-coil transition is examined critically. The first model is an all-atomic representation for a poly-alanine chain, while the second model is a minimal helix-forming model that contains no system specifics. Key characteristics of the helix-coil transition, in particular, the effective critical exponents of these two models agree with each other, within a finite-size scaling analysis.

physics.chem-ph↗
arXiv2000

Protein Folding Simulations in a Deformed Energy Landscape

A modified version of stochastic tunneling, a recently introduced global optimization technique, is introduced as a new generalized-ensemble technique and tested for a benchmark peptide, Met-enkephalin. It is demonstrated that the new technique allows to evaluate folding properties of this peptide

physics.comp-ph↗
arXiv1998

Stochastic dynamics simulations in a new generalized ensemble

We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the methods are tested with an energy function for a protein system. Simulations in this generalized ensemble by the three methods are performed for a penta peptide, Met-enkephalin. For each algorithm, it is shown that from only one simulation run one can not only find the global-minimum-energy conformation but also obtain probability distributions in canonical ensemble at any temperature, which allows the calculation of any thermodynamic quantity as a function of temperature.

physics.bio-ph↗
arXiv1998

Tertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm

We have performed multicanonical Monte Carlo simulations of C-peptide of ribonuclease A. It is known by CD and NMR experiments that this peptide has high alpha-helix content in aqueous solution and that the side-chain charges of residues Glu-2$^-$ and His-12$^+$ play an important role in the stability of the alpha-helix. In order to confirm these experimental implications, we have used two analogues of the peptide with charged and neutral side chains of Glu-2 and His-12. Two dielectric functions, distance-dependent and constant, are considered to study the effects of solvent contributions. All the simulations were started from random initial conformations. Various thermodynamic quantities such as average helicity as a function of residue number and average distance between two side chains as a function of temperature are calculated. The results are found to be in accord with the implications of CD and NMR experiments. The lowest-energy conformation obtained has an alpha-helix from Ala-4 to Gln-11 in complete agreement with the corresponding structure deduced from an X-ray crystallography experiment of ribonuclease A. It is shown that the salt bridge between the side chains of Glu-2$^-$ and Arg-10$^+$, which is known to exist from both NMR and X-ray experiments, is formed only when the side chains are properly charged. Its formation is greatly enhanced when the distance-dependent dielectric function is used.

physics.chem-ph↗
arXiv1998

Characteristic Temperatures of Folding of a Small Peptide

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the folding of a small peptide is a multi-stage process associated with two characteristic temperatures, the collapse temperature T_θ and the folding temperature T_f. Our results give supporting evidence for the energy landscape picture and funnel concept. These ideas were previously developed in the context of studies of simplified protein models, and here for the first time checked in an all-atom Monte Carlo simulation.

physics.chem-ph↗
arXiv1998

Configuration Space for Random Walk Dynamics

Applied to statistical physics models, the random cost algorithm enforces a Random Walk (RW) in energy (or possibly other thermodynamic quantities). The dynamics of this procedure is distinct from fixed weight updates. The probability for a configuration to be sampled depends on a number of unusual quantities, which are explained in this paper. This has been overlooked in recent literature, where the method is advertised for the calculation of canonical expectation values. We illustrate these points for the $2d$ Ising model. In addition, we proof a previously conjectured equation which relates microcanonical expectation values to the spectral density.

cond-mat.stat-mech↗
arXiv1997

Parallel Tempering Algorithm for Conformational Studies of Biological Molecules

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by the new method. This is demonstrated by performing simulations with high statistics for one of the simplest peptides, Met-enkephalin. The numerical effectiveness of the new technique was found to be much better than traditional methods and is comparable to sophisticated methods like generalized ensemble techniques.

physics.chem-ph↗
arXiv1997

Generalized-ensemble Monte carlo method for systems with rough energy landscape

We present a novel Monte Carlo algorithm which enhances equilibrization of low-temperature simulations and allows sampling of configurations over a large range of energies. The method is based on a non-Boltzmann probability weight factor and is another version of the so-called generalized-ensemble techniques. The effectiveness of the new approach is demonstrated for the system of a small peptide, an example of the frustrated system with a rugged energy landscape.

cond-mat↗
arXiv1997

A simple ansatz to describe thermodynamic quantities of peptides and proteins at low temperatures

We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with numerical results of an all-atoms simulation. Our approach can be used to determine the weights for a multicanonical simulation of the molecule under consideration.

cond-mat↗
arXiv1997

Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble

We demonstrate that the multicanonical approach is not restricted to Monte Carlo simulations, but can also be applied to simulation techniques such as molecular dynamics, Langevin, and hybrid Monte Carlo algorithms. The effectiveness of the methods are tested with an energy function for the protein folding problem. Simulations in the multicanonical ensemble by the three methods are performed for a penta peptide, Met-enkephalin. For each algorithm, it is shown that from only one simulation run one can not only find the global-minimum-energy conformation but also obtain probability distributions in canonical ensemble at any temperature, which allows the calculation of any thermodynamic quantity as a function of temperature.

physics.chem-ph↗
arXiv1997

Numerical Comparisons of Three Recently Proposed Algorithms in the Protein Folding Problem

We compare numerically the effectiveness of three recently proposed algorithms, multicanonical simulations, simulations in a 1/k-ensemble, and simulated tempering for the protein folding problem. For this we perform simulations with high statistics for one of the simplest peptides, Met-enkephalin. While the performances of all three approaches is much better than traditional methods, we find that the differences among the three are only marginal.

physics.chem-ph↗
arXiv1997

Variation of the Energy Landscape of a Small Peptide under a Change from the ECEPP/2 Force Field to ECEPP/3

The multicanonical ansatz is used to study variations in the energy landscape of a small peptide, Met-enkephalin, under a change from the ECEPP/2 force field to ECEPP/3. Local minima with energies up to 5 kcal/mol higher than the global minima are sampled and classified according to H-bridges and backbone angles. The distribution and relative weight for various temperatures of the minima are calculated and compared for the two force fields. We demonstrate that while there are small differences in the energy landscape our results at relevant temperatures are robust under changes between ECEPP/2 to ECEPP/3.

physics.chem-ph↗
arXiv1997

Simulated Annealing with Tsallis Weights - A Numerical Comparison

We discuss the use of Tsallis generalized mechanics in simulated annealing algorithms. For a small peptide it is shown that older implementations are not more effective than regular simulated annealing in finding ground state configurations. We propose a new implementation which leads to an improvement over regular simulated annealing.

cond-mat↗
arXiv1997

A new look at the 2D Ising model from exact partition function zeros for large lattice sizes

A general numerical method is presented to locate the partition function zeros in the complex beta plane for large lattice sizes. We apply this method to the 2D Ising model and results are reported for square lattice sizes up tp L=64. We also propose an alternative method to evaluate corrections to scaling which relies only on the leading zeros. This method is illustrated with our data.

cond-mat.stat-mech↗
arXiv1995

Thermodynamics of helix-coil transitions studied by multicanonical algorithms

Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former), valine (helix indifferent), and glycine (helix breaker). For alanine other lengths (15 and 20) are also considered in order to examine the length dependence. From one multicanonical production run with completely random initial conformations, we have obtained the lowest-energy conformations and various thermodynamic quantities (average helicity, Zimm-Bragg $s$ and $σ$ parameters, free energy differences between helix and coil states, etc.) as functions of temperature. The results confirm the fact that alanine is helix-forming, valine is helix-indifferent, and glycine is helix-breaking.

chem-ph↗