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In this paper, we propose a novel formulation to extend CNNs to two-dimensional (2D) manifolds using orthogonal basis functions, called Zernike polynomials. In many areas, geometric features play a key role in understanding scientific…
Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interations deform vesicle membrane is a fundamental question in biophysics. In this article we developed a fast algorithm to…
A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data…
Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a…
We present a procedure to approximate a plane contour by piecewise polynomial functions, depending on various parameters, such as degree, number of local patches, selection of knots. This procedure aims to be adopted to study how…
When matching parts of a surface to its whole, a fundamental question arises: Which points should be included in the matching process? The issue is intensified when using isometry to measure similarity, as it requires the validation of…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
Many factors influence biomolecules binding, and its assessment constitutes an elusive challenge in computational structural biology. In this respect, the evaluation of shape complementarity at molecular interfaces is one of the main…
Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…
Predicting the physico-chemical properties of pure substances and mixtures is a central task in thermodynamics. Established prediction methods range from fully physics-based ab-initio calculations, which are only feasible for very simple…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
Predicting protein interactions is one of the more interesting challenges of the post-genomic era. Many algorithms address this problem as a binary classification problem: given two proteins represented as two vectors of features, predict…
Segmentation of multiple surfaces in medical images is a challenging problem, further complicated by the frequent presence of weak boundary and mutual influence between adjacent objects. The traditional graph-based optimal surface…
Surface parametrization is a crucial part in various fields, having applications in computer graphic, medical imaging, scientific computing and computational engineering. The majority of surface parametrization approaches are performed on…
Statistical shape modeling is an essential tool for the quantitative analysis of anatomical populations. Point distribution models (PDMs) represent the anatomical surface via a dense set of correspondences, an intuitive and easy-to-use…
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
Fingerprints are the most widely deployed form of biometric identification. No two individuals share the same fingerprint because they have unique biometric identifiers. This paper presents an efficient fingerprint verification algorithm…
We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…