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In order to perform universal fault-tolerant quantum computation, one needs to implement a logical non-Clifford gate. Consequently, it is important to understand codes that implement such gates transversally. In this paper, we adopt an…
Orthogonal geometric constructions are the basis of many many quantum error-correcting codes (QEC), but strict orthogonality constraints limit design flexibility and resource efficiency. We introduce a quasi-orthogonal geometric framework…
The possible existence of shape-coexisting nuclear configurations with tetrahedral symmetry is receiving an increasing attention due to unprecedented nuclear structure properties, in particular in terms of the exotic 4-fold nucleonic level…
The regular polyhedra have the highest order of 3D symmetries and are exceptionally at- tractive templates for (self)-assembly using minimal types of building blocks, from nano-cages and virus capsids to large scale constructions like glass…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency,…
We study the combinatorial geometry of a random closed multicurve on a surface of large genus and of a random square-tiled surface of large genus. We prove that primitive components of a random multicurve represent linearly independent…
A formalism is developed which allows to determine the locations of all local symmetry axes of three-dimensional particles with overall icosahedral symmetry. It relies on the fact that the root system of the non-crystallographic Coxeter…
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching…
We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-stage methods that cascade structure design with amino…
The present paper is devoted to the study of the combinatorics of 216 maximal $C^3$ circular codes --- a particular type of structure arising in the analysis of genomic sequences. Their circularity property is believed to be intimately…
The structures of cyclic DNA codes of odd length over the finite rings R=Z_{4}+wZ_{4}, w^{2}=2 and S=Z_{4}+wZ_{4}+vZ_{4}+wvZ_{4},w^{2}=2,v^{2}=v,wv=vw are studied. The links between the elements of the rings R, S and 16 and 256 codons are…
We consider the Quantum Inverse Scattering Method with a new R-matrix depending on two parameters $q$ and $t$. We find that the underlying algebraic structure is the two-parameter deformed algebra $SU_{q,t}(2)$ enlarged by introducing an…
The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with…
We consider finite groups of small order for family symmetry. It is found that the binary dihedral group Q_6, along with the assumption that the Higgs sector is of type II, predicts mass matrix of a nearest neighbor interaction type for…
A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a…
Symmetric Space Sine-Gordon theories are two-dimensional massive integrable field theories, generalising the Sine-Gordon and Complex Sine-Gordon theories. To study their integrability properties on the real line, it is necessary to…
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino acids $f_{\rm core}$, packing fraction $\langle \phi\rangle$ of…
The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations thus allowing degenerate systems to exhibit a…
We present a symmetry-based approach for shape coexistence in nuclei, founded on the concept of partial dynamical symmetry (PDS). The latter corresponds to a situation when only selected states (or bands of states) of the coexisting…