4,905 research outputs found
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.Comment: Late
Studies of an Off-Lattice Model for Protein Folding: Sequence Dependence and Improved Sampling at Finite Temperature
We study the thermodynamic behavior of a simple off-lattice model for protein
folding. The model is two-dimensional and has two different ``amino acids''.
Using numerical simulations of all chains containing eight or ten monomers, we
examine the sequence dependence at a fixed temperature. It is shown that only a
few of the chains exist in unique folded state at this temperature, and the
energy level spectra of chains with different types of behavior are compared.
Furthermore, we use this model as a testbed for two improved Monte Carlo
algorithms. Both algorithms are based on letting some parameter of the model
become a dynamical variable; one of the algorithms uses a fluctuating
temperature and the other a fluctuating monomer sequence. We find that by these
algorithms one gains large factors in efficiency in comparison with
conventional methods.Comment: 17 pages, 9 Postscript figures. Combined with chem-ph/950500
Monte Carlo Study of the Phase Structure of Compact Polymer Chains
We study the phase behavior of single homopolymers in a simple
hydrophobic/hydrophilic off-lattice model with sequence independent local
interactions. The specific heat is, not unexpectedly, found to exhibit a
pronounced peak well below the collapse temperature, signalling a possible
low-temperature phase transition. The system size dependence at this maximum is
investigated both with and without the local interactions, using chains with up
to 50 monomers. The size dependence is found to be weak. The specific heat
itself seems not to diverge. The homopolymer results are compared with those
for two non-uniform sequences. Our calculations are performed using the methods
of simulated and parallel tempering. The performances of these algorithms are
discussed, based on careful tests for a small system.Comment: 13 pages LaTeX, 6 Postscript figures, References adde
The Activation-Relaxation Technique : ART nouveau and kinetic ART
The evolution of many systems is dominated by rare activated events that occur on timescale ranging from nanoseconds to the hour or more. For such systems, simulations must leave aside the full thermal description to focus specifically on mechanisms that generate a configurational change. We present here the activation relaxation technique (ART), an open-ended saddle point search algorithm, and a series of recent improvements to ART nouveau and kinetic ART, an ART-based on-the-fly off-lattice self-learning kinetic Monte Carlo method
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