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Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory…

The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the non-canonical forms A (with a narrow major groove and a large amount of…

Many real-world networks are characterized by directionality; however, the absence of an appropriate Fourier basis hinders the effective implementation of graph signal processing techniques. Inspired by discrete signal processing, where…

Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…

Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…

Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensable component of the immunological system: 2B4 is a receptor…

This work concerns formal descriptions of DNA code properties, and builds on previous work on transducer descriptions of classic code properties and on trajectory descriptions of DNA code properties. This line of research allows us to give…

Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities - for biologists…

We first prove that for every vertex x of a 4-connected graph G there exists a subgraph H in G isomorphic to a subdivision of the complete graph K4 on four vertices such that G-V(H) is connected and contains x. This implies an affirmative…

We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…

Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…

We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…

Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…

High-quality superconducting KxFeySe2 single crystals were synthesized using an easy one-step method. Detailed annealing studies were performed to make clear the phase formation process in KxFeySe2. Compatible observations were found in…

We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…

We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…

DNA frequently adopts liquid-crystalline conformations in both cells and viruses. The Oseen--Frank framework provides a powerful continuum description of these phases through three elastic moduli: splay ($K_1$), twist or cholesteric…

High-density structures of sub-surface phosphorus dopants in silicon continue to garner interest as a silicon-based quantum computer platform, however, a much-needed confirmation of their dopant arrangement has been lacking. In this work,…

Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…

Background: Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. Scope…