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Band structures of electrons in a periodic potential are well-known to host topologies that impact their behaviors at edges and interfaces. The concept however is more general than the single-electron setting. In this work, we consider…
The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards…
Positional encodings are essential to transformer-based generative models, yet their behavior in multimodal and attention-sharing settings is not fully understood. In this work, we present a principled analysis of Rotary Positional…
We design toy protein mimicking a machine-like function of an enzyme. Using an insight gained by the study of conformation space of compact lattice polymers, we demonstrate the possibility of a large scale conformational rearrangement which…
We study the electronic structure of bulk 1T-TaSe$_2$ in the charge density wave phase at low temperature. Our spatially and angle resolved photoemission (ARPES) data show insulating areas coexisting with metallic regions characterized by a…
The layered iron superconductors are discussed using electronic structure calculations. The four families of compounds discovered so far, including Fe(Se,Te) have closely related electronic structures. The Fermi surface consists of…
Electronic nematicity, a correlated state characterized by broken rotational symmetry, has been recognized as a ubiquitous feature intertwined with unconventional electron pairing in various iron-based superconductors. Here we employ…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
We report on a systematic study of the Cd, Zn, Se, and S elemental distributions across the interfaces in CdSe/Cd1-xZnxS core-shell and CdSe/CdS/Cd1-xZnxS core-crown-shell quantum wells with the CdSe core thickness ranging from 3.5 to 5.5…
Structural distortions and imperfections are a crucial aspect of materials science, on the macroscopic scale providing strength, but also enhancing corrosion and reducing electrical and thermal conductivity. At the nanometre scale,…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
High entropy alloys are a class of materials with many significant improvements in terms of mechanical properties as compared to ``classical'' alloys. The corresponding structure-property relations are not yet entirely clear, but it is…
Biological cells self-organize into living materials that uniquely blend structure with functionality and responsiveness to the environment. The integration of similar life-like features in man-made materials remains challenging, yet…
Turing patterns are fundamental in biophysics, emerging from short-range activation and long-range inhibition processes. However, their paradigm is based on diffusive transport processes, which yields Turing patters that are less sharp than…
We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways…
Flexible mechanical metamaterials possess repeating structural motifs that imbue them with novel, exciting properties including programmability, anomalous elastic moduli and nonlinear and robust response. We address such structures via…
In lattice models with quadratic finite-range Hermitian Hamiltonians, the inherently non-Hermitian transfer matrix (TM) governs the band dispersion. The van Hove singularities (VHSs) are special points in the band dispersion where the…
The electronic charge density plays a central role in determining the behavior of matter at the atomic scale, but its computational evaluation requires demanding electronic-structure calculations. We introduce an atom-centered,…