14,612 research outputs found
A topological approach for protein classification
Protein function and dynamics are closely related to its sequence and
structure. However prediction of protein function and dynamics from its
sequence and structure is still a fundamental challenge in molecular biology.
Protein classification, which is typically done through measuring the
similarity be- tween proteins based on protein sequence or physical
information, serves as a crucial step toward the understanding of protein
function and dynamics. Persistent homology is a new branch of algebraic
topology that has found its success in the topological data analysis in a
variety of disciplines, including molecular biology. The present work explores
the potential of using persistent homology as an indepen- dent tool for protein
classification. To this end, we propose a molecular topological fingerprint
based support vector machine (MTF-SVM) classifier. Specifically, we construct
machine learning feature vectors solely from protein topological fingerprints,
which are topological invariants generated during the filtration process. To
validate the present MTF-SVM approach, we consider four types of problems.
First, we study protein-drug binding by using the M2 channel protein of
influenza A virus. We achieve 96% accuracy in discriminating drug bound and
unbound M2 channels. Additionally, we examine the use of MTF-SVM for the
classification of hemoglobin molecules in their relaxed and taut forms and
obtain about 80% accuracy. The identification of all alpha, all beta, and
alpha-beta protein domains is carried out in our next study using 900 proteins.
We have found a 85% success in this identifica- tion. Finally, we apply the
present technique to 55 classification tasks of protein superfamilies over 1357
samples. An average accuracy of 82% is attained. The present study establishes
computational topology as an independent and effective alternative for protein
classification
From 3D Models to 3D Prints: an Overview of the Processing Pipeline
Due to the wide diffusion of 3D printing technologies, geometric algorithms
for Additive Manufacturing are being invented at an impressive speed. Each
single step, in particular along the Process Planning pipeline, can now count
on dozens of methods that prepare the 3D model for fabrication, while analysing
and optimizing geometry and machine instructions for various objectives. This
report provides a classification of this huge state of the art, and elicits the
relation between each single algorithm and a list of desirable objectives
during Process Planning. The objectives themselves are listed and discussed,
along with possible needs for tradeoffs. Additive Manufacturing technologies
are broadly categorized to explicitly relate classes of devices and supported
features. Finally, this report offers an analysis of the state of the art while
discussing open and challenging problems from both an academic and an
industrial perspective.Comment: European Union (EU); Horizon 2020; H2020-FoF-2015; RIA - Research and
Innovation action; Grant agreement N. 68044
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
This work introduces a number of algebraic topology approaches, such as
multicomponent persistent homology, multi-level persistent homology and
electrostatic persistence for the representation, characterization, and
description of small molecules and biomolecular complexes. Multicomponent
persistent homology retains critical chemical and biological information during
the topological simplification of biomolecular geometric complexity.
Multi-level persistent homology enables a tailored topological description of
inter- and/or intra-molecular interactions of interest. Electrostatic
persistence incorporates partial charge information into topological
invariants. These topological methods are paired with Wasserstein distance to
characterize similarities between molecules and are further integrated with a
variety of machine learning algorithms, including k-nearest neighbors, ensemble
of trees, and deep convolutional neural networks, to manifest their descriptive
and predictive powers for chemical and biological problems. Extensive numerical
experiments involving more than 4,000 protein-ligand complexes from the PDBBind
database and near 100,000 ligands and decoys in the DUD database are performed
to test respectively the scoring power and the virtual screening power of the
proposed topological approaches. It is demonstrated that the present approaches
outperform the modern machine learning based methods in protein-ligand binding
affinity predictions and ligand-decoy discrimination
A high-performance open-source framework for multiphysics simulation and adjoint-based shape and topology optimization
The first part of this thesis presents the advances made in the Open-Source software SU2,
towards transforming it into a high-performance framework for design and optimization of
multiphysics problems. Through this work, and in collaboration with other authors, a tenfold
performance improvement was achieved for some problems. More importantly, problems that
had previously been impossible to solve in SU2, can now be used in numerical optimization
with shape or topology variables. Furthermore, it is now exponentially simpler to study new
multiphysics applications, and to develop new numerical schemes taking advantage of modern
high-performance-computing systems.
In the second part of this thesis, these capabilities allowed the application of topology optimiza-
tion to medium scale fluid-structure interaction problems, using high-fidelity models (nonlinear
elasticity and Reynolds-averaged Navier-Stokes equations), which had not been done before
in the literature. This showed that topology optimization can be used to target aerodynamic
objectives, by tailoring the interaction between fluid and structure. However, it also made ev-
ident the limitations of density-based methods for this type of problem, in particular, reliably
converging to discrete solutions. This was overcome with new strategies to both guarantee and
accelerate (i.e. reduce the overall computational cost) the convergence to discrete solutions in
fluid-structure interaction problems.Open Acces
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