22,499 research outputs found
Euclidean distance geometry and applications
Euclidean distance geometry is the study of Euclidean geometry based on the
concept of distance. This is useful in several applications where the input
data consists of an incomplete set of distances, and the output is a set of
points in Euclidean space that realizes the given distances. We survey some of
the theory of Euclidean distance geometry and some of the most important
applications: molecular conformation, localization of sensor networks and
statics.Comment: 64 pages, 21 figure
GreMuTRRR: A Novel Genetic Algorithm to Solve Distance Geometry Problem for Protein Structures
Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to
predict the native structure of proteins. However, NMR machines are only able
to report approximate and partial distances between pair of atoms. To build the
protein structure one has to solve the Euclidean distance geometry problem
given the incomplete interval distance data produced by NMR machines. In this
paper, we propose a new genetic algorithm for solving the Euclidean distance
geometry problem for protein structure prediction given sparse NMR data. Our
genetic algorithm uses a greedy mutation operator to intensify the search, a
twin removal technique for diversification in the population and a random
restart method to recover stagnation. On a standard set of benchmark dataset,
our algorithm significantly outperforms standard genetic algorithms.Comment: Accepted for publication in the 8th International Conference on
Electrical and Computer Engineering (ICECE 2014
New error measures and methods for realizing protein graphs from distance data
The interval Distance Geometry Problem (iDGP) consists in finding a
realization in of a simple undirected graph with
nonnegative intervals assigned to the edges in such a way that, for each edge,
the Euclidean distance between the realization of the adjacent vertices is
within the edge interval bounds. In this paper, we focus on the application to
the conformation of proteins in space, which is a basic step in determining
protein function: given interval estimations of some of the inter-atomic
distances, find their shape. Among different families of methods for
accomplishing this task, we look at mathematical programming based methods,
which are well suited for dealing with intervals. The basic question we want to
answer is: what is the best such method for the problem? The most meaningful
error measure for evaluating solution quality is the coordinate root mean
square deviation. We first introduce a new error measure which addresses a
particular feature of protein backbones, i.e. many partial reflections also
yield acceptable backbones. We then present a set of new and existing quadratic
and semidefinite programming formulations of this problem, and a set of new and
existing methods for solving these formulations. Finally, we perform a
computational evaluation of all the feasible solverformulation combinations
according to new and existing error measures, finding that the best methodology
is a new heuristic method based on multiplicative weights updates
The LBFGS Quasi-Newtonian Method for Molecular Modeling Prion AGAAAAGA Amyloid Fibrils
Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance)
spectroscopy, dual polarization interferometry, etc are indeed very powerful
tools to determine the 3-Dimensional structure of a protein (including the
membrane protein); theoretical mathematical and physical computational
approaches can also allow us to obtain a description of the protein 3D
structure at a submicroscopic level for some unstable, noncrystalline and
insoluble proteins. X-ray crystallography finds the X-ray final structure of a
protein, which usually need refinements using theoretical protocols in order to
produce a better structure. This means theoretical methods are also important
in determinations of protein structures. Optimization is always needed in the
computer-aided drug design, structure-based drug design, molecular dynamics,
and quantum and molecular mechanics. This paper introduces some optimization
algorithms used in these research fields and presents a new theoretical
computational method - an improved LBFGS Quasi-Newtonian mathematical
optimization method - to produce 3D structures of Prion AGAAAAGA amyloid
fibrils (which are unstable, noncrystalline and insoluble), from the potential
energy minimization point of view. Because the NMR or X-ray structure of the
hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the
model constructed by this paper can be used as a reference for experimental
studies on this region, and may be useful in furthering the goals of medicinal
chemistry in this field
Numerical algebraic geometry for model selection and its application to the life sciences
Researchers working with mathematical models are often confronted by the
related problems of parameter estimation, model validation, and model
selection. These are all optimization problems, well-known to be challenging
due to non-linearity, non-convexity and multiple local optima. Furthermore, the
challenges are compounded when only partial data is available. Here, we
consider polynomial models (e.g., mass-action chemical reaction networks at
steady state) and describe a framework for their analysis based on optimization
using numerical algebraic geometry. Specifically, we use probability-one
polynomial homotopy continuation methods to compute all critical points of the
objective function, then filter to recover the global optima. Our approach
exploits the geometric structures relating models and data, and we demonstrate
its utility on examples from cell signaling, synthetic biology, and
epidemiology.Comment: References added, additional clarification
A Collection of Challenging Optimization Problems in Science, Engineering and Economics
Function optimization and finding simultaneous solutions of a system of
nonlinear equations (SNE) are two closely related and important optimization
problems. However, unlike in the case of function optimization in which one is
required to find the global minimum and sometimes local minima, a database of
challenging SNEs where one is required to find stationary points (extrama and
saddle points) is not readily available. In this article, we initiate building
such a database of important SNE (which also includes related function
optimization problems), arising from Science, Engineering and Economics. After
providing a short review of the most commonly used mathematical and
computational approaches to find solutions of such systems, we provide a
preliminary list of challenging problems by writing the Mathematical
formulation down, briefly explaning the origin and importance of the problem
and giving a short account on the currently known results, for each of the
problems. We anticipate that this database will not only help benchmarking
novel numerical methods for solving SNEs and function optimization problems but
also will help advancing the corresponding research areas.Comment: Accepted as an invited contribution to the special session on
Evolutionary Computation for Nonlinear Equation Systems at the 2015 IEEE
Congress on Evolutionary Computation (at Sendai International Center, Sendai,
Japan, from 25th to 28th May, 2015.
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