Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach
نویسندگان
چکیده
We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic Gillespie scheme with the denaturation zones in double stranded DNA studied as a single molecule time series. Simulated Annealing is used to find the optimum value of the activation energy for which the equilibrium bubble size distribution matches with a given value. It is demonstrated that the method overcomes even large noise in the input surrogate data. PACS numbers: 87.15.Av, 05.40.-a, 87.14.Gg, 02.60.Pn, 87.80.Nj Finding the optimum activation energy ... Chaudhury et al. 2
منابع مشابه
Estimation of Software Reliability by Sequential Testing with Simulated Annealing of Mean Field Approximation
Various problems of combinatorial optimization and permutation can be solved with neural network optimization. The problem of estimating the software reliability can be solved with the optimization of failed components to its minimum value. Various solutions of the problem of estimating the software reliability have been given. These solutions are exact and heuristic, but all the exact approach...
متن کاملFinding the Shortest Hamiltonian Path for Iranian Cities Using Hybrid Simulated Annealing and Ant Colony Optimization Algorithms
The traveling salesman problem is a well-known and important combinatorial optimization problem. The goal of this problem is to find the shortest Hamiltonian path that visits each city in a given list exactly once and then returns to the starting city. In this paper, for the first time, the shortest Hamiltonian path is achieved for 1071 Iranian cities. For solving this large-scale problem, tw...
متن کاملDetermining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization.
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local denaturation zones (bubbles). On the basis of the reconstructed bubble size distribution, this is achieved through stochastic optimization of the free energie...
متن کاملA New Hybrid Routing Algorithm based on Genetic Algorithm and Simulated Annealing for Vehicular Ad hoc Networks
In recent years, Vehicular Ad-hoc Networks (VANET) as an emerging technology have tried to reduce road damage and car accidents through intelligent traffic controlling. In these networks, the rapid movement of vehicles, topology dynamics, and the limitations of network resources engender critical challenges in the routing process. Therefore, providing a stable and reliable routing algorithm is ...
متن کاملImage segmentation using an annealed Hopfield neural network
Good image segmentation can be achieved by finding the optimum solution to an appropriate energy function. A liopfleld neural network has been shown to solve complex optimization problems fast, but it only guarantees convergence to a local minimum of the optimization function. Alternatively, mean field annealing has been shown to reach the global or the nearly global optimum solution when solvi...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2009