Related papers: Combinatorial RNA Design Designability and Structu…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
We develop three approaches of combinatorial flavour to study the structure of minimal codes and cutting blocking sets in finite geometry, each of which has a particular application. The first approach uses techniques from algebraic…
The development of new materials typically involves a process of trial and error, guided by insights from past experimental and theoretical findings. The inverse design approach for soft-matter systems has the potential to optimize specific…
Quantum computers are expected to enable fast solving of large-scale combinatorial optimization problems. However, their limitations in fidelity and the number of qubits prevent them from handling real-world problems. Recently, a…
Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more…
A relative t-design in the binary Hamming association schemes H(n,2) is equivalent to a weighted regular t-wise balanced design, i.e., certain combinatorial t-design which allow different sizes of blocks and a weight function on blocks. In…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Quaternary code (QC) designs form an attractive class of nonregular factorial fractions. We develop a complementary set theory for characterizing optimal QC designs that are highly fractionated in the sense of accommodating a large number…
Based on ideas of K\"otter and Kschischang we use constant dimension subspaces as codewords in a network. We show a connection to the theory of q-analogues of a combinatorial designs, which has been studied in Braun, Kerber and Laue as a…
The tensor-RPA approach developed previously in part I is applied to the Nambu-Jona-Lasinio (NJL) model. As a first step we investigate the structure of Dirac-Hartree-Fock solutions for a rotationally and isospin invariant ground-state…
Background: In the Nearest-Neighbor Thermodynamic Model, a standard approach for RNA secondary structure prediction, the energy of the multiloops is modeled using a linear entropic penalty governed by three branching parameters. Although…
In this paper we study $k$-noncrossing, canonical RNA pseudoknot structures with minimum arc-length $\ge 4$. Let ${\sf T}_{k,\sigma}^{[4]} (n)$ denote the number of these structures. We derive exact enumeration results by computing the…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
Protein design is a technique to engineer proteins by modifying their sequence to obtain novel functionalities. In this method, amino acids in the sequence are permutated to find the low energy states satisfying the configuration. However,…
In this paper, we develop new algorithms for the basic RNA folding problem. Given an RNA sequence that contains $n$ nucleotides, the goal of the problem is to compute a pseudoknot-free secondary structure that maximizes the number of base…
We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
Neural Architecture Search (NAS), aiming at automatically designing neural architectures by machines, has been considered a key step toward automatic machine learning. One notable NAS branch is the weight-sharing NAS, which significantly…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Pattern self-assembly tile set synthesis (PATS) is a combinatorial optimization problem which aim at minimizing a rectilinear tile assembly system (RTAS) that uniquely self-assembles a given rectangular pattern, and is known to be NP-hard.…