Related papers: Conformations of Macromolecules and their Complexe…

The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…

Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts…

We consider the time evolution of a one dimensional $n$-gradient continuum. Our aim is to construct and analyze discrete approximations in terms of physically realizable mechanical systems, called microscopic because they are living on a…

Accurate molecular imaging via high-order harmonic generation relies on comparing the harmonic emission from a molecule and an adequate reference system. However, an ideal reference atom with the same ionization properties as the molecule…

Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…

Homogeneous wavelets and framelets have been extensively investigated in the classical theory of wavelets and they are often constructed from refinable functions via the multiresolution analysis. On the other hand, nonhomogeneous wavelets…

Non-invasive light scattering methods provide data on biological macromolecules (i.e. proteins, nucleic acids, as well as assemblies and larger entities composed of them) that are complementary with those of size exclusion chromatography,…

Big data often has emergent structure that exists at multiple levels of abstraction, which are useful for characterizing complex interactions and dynamics of the observations. Here, we consider multiple levels of abstraction via a…

Single molecule X-ray scattering experiments with free electron lasers have opened a new route to the structure determination of biomolecules. Because typically only very few photons per scattering image are recorded and thus the…

This thesis (extended abstract) presents the software development efforts toward efficient exploitation of heterogeneity through intricate mapping of computational kernels, collaborative execution of multiple processing elements and…

Complex networks have been widely used in science and technology because of their ability to represent several systems. One of these systems is found in Biochemistry, in which the synthesis of new nanoparticles is a hot topic. However, the…

Motivated by recent best case analyses for some sorting algorithms and based on the type of complexity we partition the algorithms into two classes: homogeneous and non homogeneous algorithms. Although both classes contain algorithms with…

This paper presents a high-accuracy higher-order multiscale method for solving multi-continuum problems in in highly heterogeneous media. First, microscopic unit cell functions are defined, leading to the derivation of macroscopic…

Sparse representation-based classifiers have shown outstanding accuracy and robustness in image classification tasks even with the presence of intense noise and occlusion. However, it has been discovered that the performance degrades…

We present a novel approach for finding and evaluating structural models of small metallic nanoparticles. Rather than fitting a single model with many degrees of freedom, the approach algorithmically builds libraries of nanoparticle…

We introduce a new model for the task mapping problem to aid in the systematic design of algorithms for heterogeneous systems including, but not limited to, CPUs, GPUs and FPGAs. A special focus is set on the communication between the…

We aim to improve segmentation through the use of machine learning tools during region agglomeration. We propose an active learning approach for performing hierarchical agglomerative segmentation from superpixels. Our method combines…

Cryo-electron tomography (cryo-ET) has emerged as a powerful tool for studying the structural heterogeneity of proteins and their complexes, offering insights into macromolecular dynamics directly within cells. Driven by recent…

Microarray technology is a new and powerful tool for the concurrent monitoring of a large number of gene expressions. Each microarray experiment produces hundreds of images. Each digital image requires a large storage space. Hence,…

High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times…