Related papers: Constraint Programming Approaches to the Discretiz…
The Discretizable Molecular Distance Geometry Problem (DMDGP) aims to determine the three-dimensional protein structure using distance information from nuclear magnetic resonance experiments. The DMDGP has a finite number of candidate…
The fundamental inverse problem in distance geometry is the one of finding positions from inter-point distances. The Discretizable Molecular Distance Geometry Problem (DMDGP) is a subclass of the Distance Geometry Problem (DGP) whose search…
Given a weighted undirected graph $G=(V,E,d)$, the Molecular Distance Geometry Problem (MDGP) is that of finding a function $x:G\to \mathbb{R}^{3}$, where $||x(u)-x(v)||=d(u,v)$ for each $\{u,v\}\in E$. We show that under a few assumptions…
Given an integer dimension K and a simple, undirected graph G with positive edge weights, the Distance Geometry Problem (DGP) aims to find a realization function mapping each vertex to a coordinate in K-dimensional space such that the…
The Molecular Distance Geometry Problem (MDGP) is essential in structural biology, as it seeks to determine three-dimensional protein structures from partial interatomic distances. Its discretizable subclass (DMDGP) admits an exact…
The Discretizable Molecular Distance Geometry Problem (DMDGP) consists in a subclass of the Molecular Distance Geometry Problem for which an embedding in ${\mathbb{R}^3}$ can be found using a Branch & Prune (BP) algorithm in a discrete…
Distance Geometry plays a central role in determining protein structures from Nuclear Magnetic Resonance (NMR) data, a task known as the Molecular Distance Geometry Problem (MDGP). A subclass of this problem, the Discretizable Distance…
The Generalized Discretizable Molecular Distance Geometry Problem is a distance geometry problems that can be solved by a combinatorial algorithm called ``Branch-and-Prune''. It was observed empirically that the number of solutions of YES…
The Maximally Diverse Grouping Problem (MDGP) is the problem of assigning a set of elements to mutually disjoint groups in order to maximise the overall diversity between the elements. Because the MDGP is NP-complete, most studies have…
Geometric programming (GP) is a well-known optimization tool for dealing with a wide range of nonlinear optimization and engineering problems. In general, it is assumed that the parameters of a GP problem are deterministic and accurate.…
Distance Geometry Problem (DGP) and Nonlinear Mapping (NLM) are two well established questions: Distance Geometry Problem is about finding a Euclidean realization of an incomplete set of distances in a Euclidean space, whereas Nonlinear…
A Geometric programming (GP) is a type of mathematical problem characterized by objective and constraint functions that have a special form. Many methods have been developed to solve large scale engineering design GP problems. In this paper…
Geometric programming (GP) provides a power tool for solving a variety of optimization problems. In the real world, many applications of geometric programming (GP) are engineering design problems in which some of the problem parameters are…
The Euclidean distance geometry problem arises in a wide variety of applications, from determining molecular conformations in computational chemistry to localization in sensor networks. When the distance information is incomplete, the…
The interval Distance Geometry Problem (iDGP) consists in finding a realization in $\mathbb{R}^K$ of a simple undirected graph $G=(V,E)$ with nonnegative intervals assigned to the edges in such a way that, for each edge, the Euclidean…
We introduce and study conic geometric programs (CGPs), which are convex optimization problems that unify geometric programs (GPs) and conic optimization problems such as semidefinite programs (SDPs). A CGP consists of a linear objective…
Minimum distance constraints (minDCs) appear in many geometric optimization problems. They pose major challenges for mixed-integer nonlinear programming (MINLP) due to their reverse-convexity. We develop new algorithms for tightening…
We survey theoretical, algorithmic, and computational results at the intersection of distance geometry problems and mathematical programming, both with and without adjacencies as part of the input. While mathematical programming methods can…
An approximate formulation of a robust geometric program (RGP) as a convex program is proposed. Interest in using geometric programs (GPs) to model complex engineering systems has been growing, and this has motivated explicitly modeling the…
An important application of distance geometry to biochemistry studies the embeddings of the vertices of a weighted graph in the three-dimensional Euclidean space such that the edge weights are equal to the Euclidean distances between…