Related papers: Constrained Shape Analysis with Applications to RN…
A routine crystallography technique, crystal structure analysis, is rarely performed in computational condensed matter research. The lack of methods to identify and characterize crystal structures reliably in particle simulation data…
Local search is widely used to solve combinatorial optimisation problems and to model biological evolution, but the performance of local search algorithms on different kinds of fitness landscapes is poorly understood. Here we consider how…
In this paper, we derive new shape descriptors based on a directional characterization. The main idea is to study the behavior of the shape neighborhood under family of transformations. We obtain a description invariant with respect to…
Constrained coding plays a key role in optimizing performance and mitigating errors in applications such as storage and communication, where specific constraints on codewords are required. While non-parametric constraints have been…
One of the essential tasks in connectomics is the morphology analysis of neurons and organelles like mitochondria to shed light on their biological properties. However, these biological objects often have tangled parts or complex branching…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP). Output from MaP provides information about both pairing (via reactivities) and contact…
Evolutionary crystal structure prediction proved to be a powerful approach for studying a wide range of materials. Here, we present a specifically designed algorithm for the prediction of the structure of complex crystals consisting of…
We establish shape holomorphy results for general weakly- and hyper-singular boundary integral operators arising from second-order partial differential equations in unbounded two-dimensional domains with multiple finite-length open arcs.…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
In contrast to proteins much less attention has been focused on development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force…
RNA molecules are single-stranded analogues of DNA that can fold into various structures which influence their biological function within the cell. RNA structures can be modelled combinatorially in terms of a certain type of graph called an…
How the geometry of nano-sized confinement affects dynamics of biomaterials is interesting yet poorly understood. An elucidation of structural details upon nano-sized confinement may benefit manufacturing pharmaceuticals in biomaterial…
Recent advances in Foundation Models for Materials Science are poised to revolutionize the discovery, manufacture, and design of novel materials with tailored properties and responses. Although great strides have been made, successes have…
Classification of polarimetric synthetic aperture radar (PolSAR) images is an active research area with a major role in environmental applications. The traditional Machine Learning (ML) methods proposed in this domain generally focus on…
We study the problem of aggregating polygons by covering them with disjoint representative regions, thereby inducing a clustering of the polygons. Our objective is to minimize a weighted sum of the total area and the total perimeter of the…
The problem of image segmentation is known to become particularly challenging in the case of partial occlusion of the object(s) of interest, background clutter, and the presence of strong noise. To overcome this problem, the present paper…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…