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1. Interphase Chromatin Undergoes a Local Sol-Gel Transition upon Cell Differentiation

   https://doi.org/10.1103/PhysRevLett.126.228101  

   Eshghi, Iraj; Eaton, Jonah A.; Zidovska, Alexandra (June 2021, Physical review letters)

   null (Ed.)

   Cell differentiation, the process by which stem cells become specialized cells, is associated with chromatin reorganization inside the cell nucleus. Here, we measure the chromatin distribution and dynamics in embryonic stem cells in vivo before and after differentiation. We find that undifferentiated chromatin is less compact, more homogeneous, and more dynamic than differentiated chromatin. Furthermore, we present a noninvasive rheological analysis using intrinsic chromatin dynamics, which reveals that undifferentiated chromatin behaves like a Maxwell fluid, while differentiated chromatin shows a coexistence of fluidlike (sol) and solidlike (gel) phases. Our data suggest that chromatin undergoes a local sol-gel transition upon cell differentiation, corresponding to the formation of the more dense and transcriptionally inactive heterochromatin. 

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2. Strong-to-Weak Spontaneous Symmetry Breaking in Mixed Quantum States

   https://doi.org/10.1103/PRXQuantum.6.010344  

   Lessa, Leonardo A; Ma, Ruochen; Zhang, Jian-Hao; Bi, Zhen; Cheng, Meng; Wang, Chong (March 2025, PRX Quantum)

   Symmetry in mixed quantum states can manifest in two distinct forms: , where each individual pure state in the quantum ensemble is symmetric with the same charge, and , which applies only to the entire ensemble. This paper explores a novel type of spontaneous symmetry breaking (SSB) where a strong symmetry is broken to a weak one. While the SSB of a weak symmetry is measured by the long-ranged two-point correlation function, the strong-to-weak SSB (SWSSB) is measured by the . We prove that SWSSB is a universal property of mixed-state quantum phases, in the sense that the phenomenon of SWSSB is robust against symmetric low-depth local quantum channels. We also show that the symmetry breaking is “spontaneous” in the sense that the effect of a local symmetry-breaking measurement cannot be recovered locally. We argue that a thermal state at a nonzero temperature in the canonical ensemble (with fixed symmetry charge) should have spontaneously broken strong symmetry. Additionally, we study nonthermal scenarios where decoherence induces SWSSB, leading to phase transitions described by classical statistical models with bond randomness. In particular, the SWSSB transition of a decohered Ising model can be viewed as the “ungauged” version of the celebrated toric-code decodability transition. We confirm that, in the decohered Ising model, the SWSSB transition defined by the fidelity correlator is the only physical transition in terms of channel recoverability. We also comment on other (inequivalent) definitions of SWSSB, through correlation functions with higher Rényi indices. Published by the American Physical Society2025 

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3. Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation

   https://doi.org/10.1098/rsif.2020.0500  

   Huang, Bin; Lu, Mingyang; Galbraith, Madeline; Levine, Herbert; Onuchic, Jose N.; Jia, Dongya (August 2020, Journal of The Royal Society Interface)

   null (Ed.)

   Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To address this question, we applied a recently developed computational method, ra ndom ci rcuit pe rturbation (RACIPE), to a nine-component gene regulatory network (GRN) governing stemness, from which we identified robust gene states. Among them, four out of the five most probable gene states exhibit gene expression patterns observed in single mouse embryonic cells at 32-cell and 64-cell stages. These gene states can be robustly predicted by the stemness GRN but not by randomized versions of the stemness GRN. Strikingly, we found a hierarchical structure of the GRN with the Oct4/Cdx2 motif functioning as the first decision-making module followed by Gata6/Nanog. We propose that stem cell populations, instead of being viewed as all having a specific cellular state, can be regarded as a heterogeneous mixture including cells in various states. Upon perturbations by external signals, stem cells lose the capacity to access certain cellular states, thereby becoming differentiated. The new gene states and key parameters regulating transitions among gene states proposed by RACIPE can be used to guide experimental strategies to better understand differentiation and design reprogramming. The findings demonstrate that the functions of the stemness GRN is mainly determined by its well-evolved network topology rather than by detailed kinetic parameters. 

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4. A hybrid stochastic–deterministic mechanochemical model of cell polarization

   https://doi.org/10.1091/mbc.E19-09-0549  

   Copos, Calina; Mogilner, Alex (July 2020, Molecular Biology of the Cell)

   Edelstein-Keshet, Leah (Ed.)

   Polarization is a crucial component in cell differentiation, development, and motility, but its details are not yet well understood. At the onset of cell locomotion, cells break symmetry to form well-defined cell fronts and rears. This polarity establishment varies across cell types: in Dictyostelium discoideum cells, it is mediated by biochemical signaling pathways and can function in the absence of a cytoskeleton, while in keratocytes, it is tightly connected to cytoskeletal dynamics and mechanics. Theoretical models that have been developed to understand the onset of polarization have explored either signaling or mechanical pathways, yet few have explored mechanochemical mechanisms. However, many motile cells rely on both signaling modules and actin cytoskeleton to break symmetry and achieve a stable polarized state. We propose a general mechanochemical polarization model based on coupling between a stochastic model for the segregation of signaling molecules and a simplified mechanical model for actin cytoskeleton network competition. We find that local linear coupling between minimally nonlinear signaling and cytoskeletal systems, separately not supporting stable polarization, yields a robustly polarized cell state. The model captures the essence of spontaneous polarization of neutrophils, which has been proposed to emerge due to the competition between frontness and backness pathways. 

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5. Symmetry-Enforced Many-Body Separability Transitions

   https://doi.org/10.1103/PRXQuantum.5.030310  

   Chen, Yu-Hsueh; Grover, Tarun (July 2024, PRX Quantum)

   We study quantum many-body mixed states with a symmetry from the perspective of , i.e., whether a mixed state can be expressed as an ensemble of short-range-entangled symmetric pure states. We provide evidence for “symmetry-enforced separability transitions” in a variety of states, where in one regime the mixed state is expressible as a convex sum of symmetric short-range-entangled pure states, while in the other regime, such a representation is not feasible. We first discuss the Gibbs state of Hamiltonians that exhibit spontaneous breaking of a discrete symmetry, and argue that the associated thermal phase transition can be thought of as a symmetry-enforced separability transition. Next we study cluster states in various dimensions subjected to local decoherence, and identify several distinct mixed-state phases and associated separability phase transitions, which also provides an alternative perspective on recently discussed “average symmetry-protected topological order.” We also study decohered $p+ip$superconductors, and find that if the decoherence breaks the fermion parity explicitly, then the resulting mixed state can be expressed as a convex sum of nonchiral states, while a fermion parity–preserving decoherence results in a phase transition at a nonzero threshold that corresponds to spontaneous breaking of fermion parity. Finally, we briefly discuss systems that satisfy the no low-energy trivial state property, such as the recently discovered good low-density parity-check codes, and argue that the Gibbs state of such systems exhibits a temperature-tuned separability transition. Published by the American Physical Society2024 

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