PACKMOL: A package for building initial configurations for molecular dynamics simulations

L Martínez, R Andrade, EG Birgin… - Journal of …, 2009 - Wiley Online Library
Adequate initial configurations for molecular dynamics simulations consist of arrangements
of molecules distributed in space in such a way to approximately represent the system's …

[图书][B] Computational methods for inverse problems

CR Vogel - 2002 - SIAM
The field of inverse problems has experienced explosive growth in the last few decades.
This is due in part to the importance of applications, like biomedical and seismic imaging …

Stress-based topology optimization for continua

C Le, J Norato, T Bruns, C Ha, D Tortorelli - Structural and Multidisciplinary …, 2010 - Springer
We propose an effective algorithm to resolve the stress-constrained topology optimization
problem. Our procedure combines a density filter for length scale control, the solid isotropic …

Nonmonotone spectral projected gradient methods on convex sets

EG Birgin, JM Martínez, M Raydan - SIAM Journal on Optimization, 2000 - SIAM
Nonmonotone projected gradient techniques are considered for the minimization of
differentiable functions on closed convex sets. The classical projected gradient schemes are …

Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking

JM Martínez, L Martínez - Journal of computational chemistry, 2003 - Wiley Online Library
Molecular Dynamics is a powerful methodology for the comprehension at molecular level of
many chemical and biochemical systems. The theories and techniques developed for …

A trust-region framework for managing the use of approximation models in optimization

NM Alexandrov, JE Dennis Jr, RM Lewis… - Structural …, 1998 - Springer
This paper presents an analytically robust, globally convergent approach to managing the
use of approximation models of varying fidelity in optimization. By robust global behaviour …

[图书][B] Optimal quadratic programming algorithms: with applications to variational inequalities

Z Dostál - 2009 - books.google.com
Solving optimization problems in complex systems often requires the implementation of
advanced mathematical techniques. Quadratic programming (QP) is one technique that …

Newton's method for large bound-constrained optimization problems

CJ Lin, JJ Moré - SIAM Journal on Optimization, 1999 - SIAM
We analyze a trust region version of Newton's method for bound-constrained problems. Our
approach relies on the geometry of the feasible set, not on the particular representation in …

Algorithm 813: SPG—software for convex-constrained optimization

EG Birgin, JM Martínez, M Raydan - ACM Transactions on Mathematical …, 2001 - dl.acm.org
Fortran 77 software implementing the SPG method is introduced. SPG is a nonmonotone
projected gradient algorithm for solving large-scale convex-constrained optimization …

A new active set algorithm for box constrained optimization

WW Hager, H Zhang - SIAM Journal on Optimization, 2006 - SIAM
An active set algorithm (ASA) for box constrained optimization is developed. The algorithm
consists of a nonmonotone gradient projection step, an unconstrained optimization step, and …