Recent results on assigned and unassigned distance geometry with applications to protein molecules and nanostructures
In the 2 years since our last 4OR review of distance geometry methods with applications to
proteins and nanostructures, there has been rapid progress in treating uncertainties in the …
proteins and nanostructures, there has been rapid progress in treating uncertainties in the …
The referenced vertex ordering problem: theory, applications, and solution methods
J Omer, A Mucherino - Open Journal of Mathematical Optimization, 2021 - numdam.org
We introduce the referenced vertex ordering problem (revorder) as a combinatorial decision
problem generalizing several vertex ordering problems that already appeared in the …
problem generalizing several vertex ordering problems that already appeared in the …
On distance graph coloring problems
R de Freitas, B Dias, N Maculan… - International …, 2021 - Wiley Online Library
One of the most important classes of combinatorial optimization problems is graph coloring,
and there are several variations of this general problem involving additional constraints …
and there are several variations of this general problem involving additional constraints …
The coherent multi-representation problem with applications in structural biology
A Mucherino - International Work-Conference on Bioinformatics and …, 2023 - Springer
Abstract We introduce the Coherent Multi-representation Problem (CMP), whose solutions
allow us to observe simultaneously different geometrical representations for the vertices of a …
allow us to observe simultaneously different geometrical representations for the vertices of a …
An efficient exhaustive search for the discretizable distance geometry problem with interval data
A Mucherino, JH Lin - 2019 Federated Conference on …, 2019 - ieeexplore.ieee.org
The Distance Geometry Problem (DGP) asks whether a simple weighted undirected graph
can be realized in a given space (generally Euclidean) so that a given set of distance …
can be realized in a given space (generally Euclidean) so that a given set of distance …
A coarse-grained representation for discretizable distance geometry with interval data
We propose a coarse-grained representation for the solutions of discretizable instances of
the Distance Geometry Problem (DGP). In several real-life applications, the distance …
the Distance Geometry Problem (DGP). In several real-life applications, the distance …
MD-JEEP: a new release for discretizable distance geometry problems with interval data
With the most recent releases of MD-JEEP, new relevant features have been included to our
software tool. MD-JEEP solves instances of the class of Discretizable Distance Geometry …
software tool. MD-JEEP solves instances of the class of Discretizable Distance Geometry …
A least-squares approach for discretizable distance geometry problems with inexact distances
DS Gonçalves - Optimization Letters, 2020 - Springer
A branch-and-prune (BP) algorithm is presented for the discretizable distance geometry
problem in R^ K RK with inexact distances. The algorithm consists in a sequential buildup …
problem in R^ K RK with inexact distances. The algorithm consists in a sequential buildup …
An integer programming approach for the search of discretization orders in distance geometry problems
J Omer, DS Gonçalves - Optimization Letters, 2020 - Springer
Discretizable distance geometry problems (DDGPs) constitute a class of graph realization
problems where the vertices can be ordered in such a way that the search space of possible …
problems where the vertices can be ordered in such a way that the search space of possible …
The K-discretization and K-incident graphs for discretizable Distance Geometry
Abstract The Distance Geometry Problem (DGP) is the problem of determining whether a
realization for a simple weighted undirected graph G=(V, E, d) G=(V, E, d) in a given …
realization for a simple weighted undirected graph G=(V, E, d) G=(V, E, d) in a given …