Dynamic program

Procacci P, Darden T A, Paci E and Marchi M 1997 ORAC a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions J. Comput. Chem. 18 1848-62... 

Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kale, L., Skeel, R.D., Schul-ten, K. NAMD - A parallel, object-oriented molecular dynamics program. Int. J. Supercomputing Applications and High Performance Computing 10 (1996) 251-268. 

Madura et al. 1995] Madura, J.D., Briggs, J.M., Wade, R.C., Davis, M.E., Luty, B.A., Ilin, A., Antosiewicz, J., Gilson, M.K., Bagheri, B., Scott, L.R., McCammon, J.A. Electrostatics and Diffusion of Molecules in Solution Simulations with the University of Houston Brownian Dynamics Program. Comp. Phys. Comm. 91 (1995) 57-95... 

J. A. Electrostatics and disffusion of molecules in solution simulations with the university of houston brownian dynamics program. Comp. Phys. Commun. 91 (1996) 57-95. 

K. Schulten. NAMD—a parallel, object-oriented molecular dynamics program. Inti. J. Supercomput. Applies. High Performance Computing, 10 251-268, 1996. 

Y. Hwang, R. Das, F. H. Saltz, M. Hadoscek and B. R. Brooks, Parallelizing molecular dynamics programs for distributed-memory machines , IEEE Computational Science and Engineering, Vol 2, no 2, 18-29, 1995. 

Fig. 10.16 Finding the optimal sequence alignment using dynamic programming with a scoring scheme in which a match scores 1, a mismatch scores —1 and the gap penalty is —2.

Lcularly popular [Taylor and Orengo 1989], The method is so named because it uses two amic programming steps. In the first step, it is necessary to determine the score for each of residues, one from each structure. These scores are used to fill a rectangular H matrix, irich dynamic programming is applied to determine the optimal alignment. 

Dynamic programming Technique widely used in sequence alignment... 

Although the Arrhenius equation does not predict rate constants without parameters obtained from another source, it does predict the temperature dependence of reaction rates. The Arrhenius parameters are often obtained from experimental kinetics results since these are an easy way to compare reaction kinetics. The Arrhenius equation is also often used to describe chemical kinetics in computational fluid dynamics programs for the purposes of designing chemical manufacturing equipment, such as flow reactors. Many computational predictions are based on computing the Arrhenius parameters. 

With many variables and constraints, linear and nonlinear programming may be applicable, as well as various numerical gradient search methods. Maximum principle and dynamic programming are laborious and have had only limited applications in this area. The various mathematical techniques are explained and illustrated, for instance, by Edgar and Himmelblau Optimization of Chemical Processes, McGraw-Hill, 1988). 

Minimum reactor volumes of isothermal and nonisothermal cascades by dynamic programming... 

L.M. Taylor and D.P. Flanagan, PRONTO 2D A Two-Dimensional Transient Solid Dynamics Program, SAND86-0594, Sandia National Laboratories, Albuquerque, NM, 87185, 1987. 

In the second step, the spatial restraints and the CHARMM22 force field tenns enforcing proper stereochemistry [80,81] are combined into an objective function. The general form of the objective function is similar to that in molecular dynamics programs such as CHARMM22 [80]. The objective function depends on the Cartesian coordinates of —10,000 atoms (3D points) that form a system (one or more molecules) ... 

A Sail, TL Blundell. Definition of general topological equivalence m protein structures A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 212 403-428, 1990. 

The sum in Eq. (43) can be obtained by a recursion algorithm used commonly in dynamic programming [62]. 

ME Davis, JD Madura, BA Luty, JA McCammon. Electrostatics and diffusion of molecules m solution Simulations with the University of Houston Brownian dynamics program. Comput Phys Commun 62 187-197, 1991. 

An alternative procedure is the dynamic programming method of Bellman (1957) which is based on the principle of optimality and the imbedding approach. The principle of optimality yields the Hamilton-Jacobi partial differential equation, whose solution results in an optimal control policy. Euler-Lagrange and Pontrya-gin s equations are applicable to systems with non-linear, time-varying state equations and non-quadratic, time varying performance criteria. The Hamilton-Jacobi equation is usually solved for the important and special case of the linear time-invariant plant with quadratic performance criterion (called the performance index), which takes the form of the matrix Riccati (1724) equation. This produces an optimal control law as a linear function of the state vector components which is always stable, providing the system is controllable. 

Bellman, R. (1957) Dynamic Programming, Princeton University Press, Princeton, NJ. 

Data from Thermal Building-Dynamics Programs... 

In many cases, some boundary conditions are not well known or not known at all. Temperature boundary conditions can be obtained from thermal building-dynamics programs that allow the capture of spatial mean temperatures during a time period as long as a whole year. Some of these programs yield surface temperature values (e.g., TRNSYS), which can be used as temperature boundary conditions at the time of CFD study. 

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