Related papers: A fast algorithm for backbones
As computers get faster, researchers -- not hardware or algorithms -- become the bottleneck in scientific discovery. Computational study of colloidal self-assembly is one area that is keenly affected: even after computers generate massive…
We consider a generic representation problem of internal coordinates (bond lengths, valence angles, and dihedral angles) and their transformation to 3-dimensional Cartesian coordinates of a biomolecule. We show that the…
Higher-dimensional orthogonal packing problems have a wide range of practical applications, including packing, cutting, and scheduling. Previous efforts for exact algorithms have been unable to avoid structural problems that appear for…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
Confocal microscopy of colloids combined with digital image processing has become a powerful tool in soft matter physics and materials science. Together, these techniques enable locating and tracking of more than half a million individual…
We study the backbone connecting two given sites of a two-dimensional lattice separated by an arbitrary distance $r$ in a system of size $L$. We find a scaling form for the average backbone mass: $<M_B>\sim L^{d_B}G(r/L)$, where $G$ can be…
The protein backbone is described as a smooth curved and twisted line in three-dimensional (3D) space and characterized by its curvature $\kappa(s)$ and torsion $\tau(s)$ both expressed as a function of arc length s. It is shown that the…
A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The…
Super-resolution reconstruction techniques entail the utilization of software algorithms to transform one or more sets of low-resolution images captured from the same scene into high-resolution images. In recent years, considerable…
In this work we apply a highly efficient Monte Carlo algorithm recently proposed by Newman and Ziff to treat percolation problems. The site and bond percolation are studied on a number of lattices in two and three dimensions. Quite good…
A novel search method for large polarization kernels is proposed. The algorithm produces a kernel with given partial distances by employing the depth-first search combined with the computation of coset leaders weight tables and sufficient…
The problem of finding dense components of a graph is a widely explored area in data analysis, with diverse applications in fields and branches of study including community mining, spam detection, computer security and bioinformatics. This…
Deep learning approaches have produced substantial breakthroughs in fields such as image classification and natural language processing and are making rapid inroads in the area of protein design. Many generative models of proteins have been…
Skeletonization extracts thin representations from images that compactly encode their geometry and topology. These representations have become an important topological prior for preserving connectivity in curvilinear structures, aiding…
Many real-world networks exhibit a multicores-periphery structure, with densely connected vertices in multiple cores surrounded by a general periphery of sparsely connected vertices. Identification of the multicores-periphery structure can…
An algorithm is presented for constructing high-order signed distance fields for two phase materials imaged with computed tomography. The signed distance field is high-order in that it is free of the quantization artifact associated with…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
We consider directed percolation with an absorbing boundary in 1+1 and 2+1 dimensions. The distribution of cluster lifetimes and sizes depend on the boundary. The new scaling exponents can be related to the exponents characterizing standard…
We present a new fast online clustering algorithm that reliably recovers arbitrary-shaped data clusters in high throughout data streams. Unlike the existing state-of-the-art online clustering methods based on k-means or k-medoid, it does…
Many matching, tracking, sorting, and ranking problems require probabilistic reasoning about possible permutations, a set that grows factorially with dimension. Combinatorial optimization algorithms may enable efficient point estimation,…