A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method

1989 ◽  
Vol 3 (2) ◽  
pp. 85-94 ◽  
Author(s):  
H. Kawai ◽  
T. Kikuchi ◽  
Y. Okamoto
Keyword(s):  
Monte Carlo ◽  
Simulated Annealing ◽  
Tertiary Structures ◽  
Simulated Annealing Method ◽  
Monte Carlo Simulated Annealing ◽  
Annealing Method

TACKLING THE MULTIPLE-MINIMA PROBLEM IN PROTEIN FOLDING BY MONTE CARLO SIMULATED ANNEALING AND GENERALIZED-ENSEMBLE ALGORITHMS

1999 ◽  
Vol 10 (08) ◽  
pp. 1571-1582 ◽  
Author(s):  
YUKO OKAMOTO
Keyword(s):  
Monte Carlo ◽  
Simulated Annealing ◽  
Sequence Information ◽  
Tertiary Structures ◽  
C Peptide ◽  
Pancreatic Trypsin Inhibitor ◽  
Multiple Minima ◽  
Monte Carlo Simulated Annealing ◽  
Α Helix ◽  
Ensemble Algorithms

Monte Carlo simulations based on simulated annealing and multicanonical algorithm have been performed to predict the secondary and tertiary structures of oligopeptide systems. Two oligopeptides, C-peptide of ribonuclease A and the fragment BPTI(16-36) of bovine pancreatic trypsin inhibitor, were studied. Only the amino-acid sequence information was used as input and initial conformations were randomly generated. The lowest-energy conformations obtained have α-helix structure and β-sheet structure for C-peptide and BPTI(16-36), respectively, in remarkable agreement with experimental results.

A simulation study of self-assembly of ABC star terpolymers confined between two parallel surfaces

Soft Matter ◽  
2021 ◽  
Author(s):  
Zhiyao Liu ◽  
Zheng Wang ◽  
Yuhua Yin ◽  
Run Jiang ◽  
Baohui Li
Keyword(s):  
Simulated Annealing ◽  
Phase Behavior ◽  
Phase Diagrams ◽  
Simulation Study ◽  
Self Assembly ◽  
Simulated Annealing Method ◽  
Parallel Surfaces ◽  
Annealing Method

Phase behavior of ABC star terpolymers confined between two identical parallel surfaces is systematically studied with a simulated annealing method. Several phase diagrams are constructed for systems with different bulk...

Component Rearrangement on Printed Wiring Boards to Maximize the Fundamental Natural Frequency

1993 ◽  
Vol 115 (3) ◽  
pp. 312-321 ◽  
Author(s):  
Tien-Sheng Chang ◽  
E. B. Magrab
Keyword(s):  
Simulated Annealing ◽  
Boundary Conditions ◽  
Natural Frequency ◽  
Printed Wiring Board ◽  
Computationally Efficient ◽  
Additional Increase ◽  
Simulated Annealing Method ◽  
Fundamental Natural Frequency ◽  
Rearrangement Algorithm ◽  
Annealing Method

A methodology to attain the highest fundamental natural frequency of a printed wiring board by rearranging its components has been developed. A general two-dimensional rearrangement algorithm is developed by which the rearrangement of the component-lead-board (CLB) assemblies is performed automatically for any combination of equal size, unequal size, movable and immovable CLBs. This algorithm is also capable of incorporating two design restrictions: fixed (immovable) components and prohibited (non-swappable) areas. A highly computationally efficient objective function for the evaluation of the automatic rearrangement process is introduced, which is a linear function of the size of the individual CLBs that have been selected for each interchange. The simulated annealing method is adapted to solve the combinatorial rearrangement of the CLBs. Using 61 combinations of boundary conditions, equal and unequal sized CLBs, movable and immovable CLBs, various CLB groupings and sets of material properties, it is found that, when compared to the exact solution obtained by an exhaustive search method, the simulated annealing method obtained the highest fundamental natural frequency within 1 percent for 87 percent of the cases considered, within 0.5 percent for 72 percent of the cases and the true maximum in 43 percent of them. To further increase the fundamental natural frequency the introduction of a single interior point support is analyzed. Depending on the boundary conditions an additional increase in the maximum fundamental natural frequency of 44 to 198 percent can be obtained.

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