Related papers: Combinatorial RNA Design Designability and Structu…
A (q,k,t)-design matrix is an m x n matrix whose pattern of zeros/non-zeros satisfies the following design-like condition: each row has at most q non-zeros, each column has at least k non-zeros and the supports of every two columns…
Like the letters in the alphabet forming words, reusing components of a heterogeneous mixture is an efficient strategy for assembling a large number of target structures. Examples range from synthetic DNA origami to proteins self-assembling…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n^3) time using Nussinov's dynamic programming algorithm. The Four-Russians method…
Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is…
The implementation of adaptive genetic algorithms (AGA) for optimization problems has proven to be superior than many other methods due to its nature of producing more robust and high quality solutions. Considering the complexity involved…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative…
The Abstraction and Reasoning Corpus (ARC) evaluates general reasoning capabilities that are difficult for both machine learning models and combinatorial search methods. We propose a neuro-symbolic approach that combines a transformer for…
Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling…
Arc-annotated sequences are useful for representing structural information of RNAs and have been extensively used for comparing RNA structures in both terms of sequence and structural similarities. Among the many paradigms referring to…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Truss optimization is a rich research field receiving renewed interest in limiting the carbon emissions of construction. However, a persistent challenge has been to construct highly optimized and often complex designs. This contribution…
Design automation in general, and in particular logic synthesis, can play a key role in enabling the design of application-specific Binarized Neural Networks (BNN). This paper presents the hardware design and synthesis of a purely…
In 'An asymptotic result on compressed sensing matrices', a new construction for compressed sensing matrices using combinatorial design theory was introduced. In this paper, we use deterministic and probabilistic methods to analyse the…
We incorporate realistic pair potential energies directly into a non-linear least-square fit of diffraction data to quantitatively compare structure models with experiment for the Ni-rich $d$(AlNiCo) quasicrystal. The initial structure…
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe…
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and…