arXiv subjects

Yair Augusto Gutiérrez Fosado

Publications and source records attributed to Yair Augusto Gutiérrez Fosado.

3 recordsLinked to original sources

arXiv2026

Topological Signatures of Hardness and Structural Order in Network-Forming Materials

Understanding how the topology of network forming materials influences their physical properties remains a longstanding challenge. Here, we investigate the topology of experimentally compatible atomistic models of amorphous silica together with the crystalline polymorphs cristobalite and quartz. By comparing multiple atomistic models of amorphous silica that equally reproduce neutron-scattering data, we show that different microscopic descriptions can imply different topological interpretations of glass stability. To characterize the network beyond conventional geometric descriptors, we introduce the linking valence, which quantifies the average number of topological links per network loop. This topological descriptor separates silica into two distinct classes: the mechanically harder quartz exhibit values more than an order of magnitude larger than those of amorphous silica and cristobalite, despite their common tetrahedral building blocks. Spectral analysis of the loop-linking networks provides a complementary distinction, separating amorphous from crystalline phases and revealing differences in the long-range organization of topological constraints. These results establish topological linking as a new framework for connecting the structure and physical properties of network-forming materials.

cond-mat.mtrl-sci↗

arXiv2025

Modulation of DNA rheology by a transcription factor that forms aging microgels

Proteins and nucleic acids form non-Newtonian liquids with complex rheological properties that contribute to their function in vivo. Here we investigate the rheology of the transcription factor NANOG, a key protein in sustaining embryonic stem cell self-renewal. We discover that at high concentrations NANOG forms macroscopic aging gels through its intrinsically disordered tryptophan-rich domain. By combining molecular dynamics simulations, mass photometry and Cryo-EM, we also discover that NANOG forms self-limiting micelle-like clusters which expose their DNA-binding domains. In dense solutions of DNA, NANOG micelle-like structures stabilize intermolecular entanglements and crosslinks, forming microgel-like structures. Our findings suggest that NANOG may contribute to regulate gene expression in a unconventional way: by restricting and stabilizing genome dynamics at key transcriptional sites through the formation of an aging microgel-like structure, potentially enabling mechanical memory in the gene network.

cond-mat.soft↗

arXiv2024

Link to Densify: Topological Transitions and Origin of Hysteresis During the (De)Compression of Amorphous Ices

In this Letter we study the phase transition between amorphous ices and the nature of the hysteresis cycle separating them. We discover that a topological transition takes place as the system transforms from low-density amorphous ice (LDA) at low pressures, to high-density amorphous ice (HDA) at high pressures. Specifically, we uncover that the hydrogen bond network (HBN) displays qualitatively different topologies in the LDA and HDA phases: the former characterised by disentangled loop motifs, while the latter displaying topologically complex and metastable Hopf-linked and knotted configurations. At the phase transition, the transient opening of the HBN topological motifs yields mechanical fragility on the macroscale. Our results provide a detailed microscopic description of the topological nature of the phase transition and the hysteresis cycle between amorphous ices. We argue that the topological transition discovered in this work may not only improve our understanding of amorphous ices but represent a generic mechanism for the densification of network-forming materials.

cond-mat.dis-nn↗