arXiv subjects

Hong-Yan Shih

Publications and source records attributed to Hong-Yan Shih.

11 recordsLinked to original sources

arXiv2026

Effective hyperuniformity in time-integrated stochastic Turing patterns

Demographic noise generates stochastic Turing patterns even when reaction-diffusion systems are deterministically stable. We show analytically and verify numerically in the Levin-Segel model that temporal integration of configurations reveals emergent large-scale organization. The intensive number variance in a window of size $R \gg 1$ approaches a finite reaction-kinetic floor as $1/R$, over a spatial range growing by orders of magnitude near the Turing instability. This yields an effectively hyperuniform, fine-tuning-free regime previously unidentified in non-conserved multispecies stochastic systems.

cond-mat.stat-mech↗

arXiv2026

Diffusion disorder in the contact process

We study the effects of spatially inhomogeneous diffusion on the non-equilibrium phase transition in the contact process. The directed-percolation critical point in the contact process is known to be stable against the addition of a spatially uniform diffusion term. Correspondingly, we find quenched randomness in the diffusion rates to be irrelevant by power counting in the field-theory of the contact process. However, large-scale Monte Carlo simulations demonstrate that such diffusion disorder destabilizes the clean directed percolation critical point. Instead, the transition belongs to the same infinite-randomness universality class as the contact process with disorder in the infection or healing rates. To explain these results, we develop an effective model with an infinite diffusion rate; it shows that diffusion disorder generates an effective disorder in the healing rates. The same mechanism also appears in the field-theoretic description: Whereas diffusion disorder is irrelevant by power-counting, it generates standard random-mass disorder under renormalization. We discuss the validity of this mechanism for other absorbing state transitions and non-equilibrium phase transitions in general.

cond-mat.stat-mech↗

arXiv2025

Diffusive Epidemic Process with quenched disorder

Epidemic spreading often occurs in spatially heterogeneous environments, yet how quenched heterogeneity reshapes its onset and critical dynamics remains poorly understood. The diffusive epidemic process, a minimal reaction-diffusion model whose absorbing-state transition is controlled by the relative diffusion of healthy and infected species, provides a natural setting for this question. Using a new single-seed algorithm that effectively simulate infinite systems for the infected individuals, we find that effective global diffusion rates can be used to predict disorder relevance and we identify two distinct infinite-disorder fixed points. Notably, we find that disorder in diffusion rates is qualitatively different from that in reaction rates as it can even induce a total suppression of the active phase, a phenomenon not observed with other types of disorder. These results establish mobility disorder as a distinct route by which quenched heterogeneity qualitatively reorganizes spreading dynamics, with implications for systems ranging from cell polarity to epidemic propagation in heterogeneous media.

cond-mat.stat-mech↗

arXiv2024

Conformations, Dynamics, and Looping Kinetics of Partially Active Polymers

We investigate the conformational and dynamical properties of a partially active Rouse chain, where activity is localized within a specific segment, positioned at various locations along the chain and spanning any given length. Through analytical methods and simulations, we reveal how the location and size of the active segment influence polymer swelling patterns. Likewise, we observe that the mean squared distance between two points along the polymer, as well as the mean squared displacement of a tagged point, are notably affected by the local activity. In addition, the reconfiguration and looping dynamics show anomalous scaling behaviors, particularly in intermediate chain lengths, capturing the interplay between persistence of active motion and polymer relaxation dynamics. Our model, relevant to spatially varying activity observed in active biopolymeric systems, provides a basis for exploring more realistic models of chromatin behavior, especially those incorporating heterogeneous activity.

cond-mat.soft↗

arXiv2019

Mechanisms of rapid evolution

The purpose of this roadmap article is to draw attention to a paradigm shift in our understanding of evolution towards a perspective of ecological-evolutionary feedback, highlighted through two recent highly simplified examples of rapid evolution. The first example focuses primarily on population dynamics: anomalies in population cycles can reflect the influence of strong selection and the interplay with mutations. The second focuses primarily on the way in which ecological structure can potentially be influenced by what is arguably the most powerful source of genetic novelty: horizontal gene transfer. We review the status of rapid evolution and also enumerate the current and future challenges of achieving a full understanding of rapid evolution in all its manifestations.

q-bio.PE↗

arXiv2018

Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution

Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in populations from microbes to higher animals. Phenotypic fluctuations can provide a basis for adaptation and be the target of selection. Here we present a theoretical and experimental investigation of the fate of phenotypic fluctuations in directed evolution experiments where phenotypes are subject to constraints. We show that selecting bacterial populations for fast migration through a porous environment drives a reduction in cell-to-cell variation across the population. Using sequencing and genetic engineering we study the genetic basis for this reduction in phenotypic fluctuations. We study the generality of this reduction by developing a simple, abstracted, numerical simulation model of the evolution of phenotypic fluctuations subject to constraints. Using this model we find that strong and weak selection generally lead respectively to increasing or decreasing cell-to-cell variation as a result of a bound on the selected phenotype under a wide range of parameters. However, other behaviors are also possible, and we describe the outcome of selection simulations for different model parameters and suggest future experiments. We analyze the mechanism of the observed reduction of phenotypic fluctuations in our experimental system, discuss the relevance of our abstract model to the experiment and explore its broader implications for evolution.

q-bio.PE↗

arXiv2016

Turbulence as a problem in non-equilibrium statistical mechanics

The transitional and well-developed regimes of turbulent shear flows exhibit a variety of remarkable scaling laws that are only now beginning to be systematically studied and understood. In the first part of this article, we summarize recent progress in understanding the friction factor of turbulent flows in rough pipes and quasi-two-dimensional soap films, showing how the data obey a two-parameter scaling law known as roughness-induced criticality, and exhibit power-law scaling of friction factor with Reynolds number that depends on the precise form of the nature of the turbulent cascade. These results hint at a non-equilibrium fluctuation-dissipation relation that applies to turbulent flows. The second part of this article concerns the lifetime statistics in smooth pipes around the transition, showing how the remarkable super-exponential scaling with Reynolds number reflects deep connections between large deviation theory, extreme value statistics, directed percolation and the onset of coexistence in predator-prey ecosystems. Both these phenomena reflect the way in which turbulence can be fruitfully approached as a problem in non-equilibrium statistical mechanics.

physics.flu-dyn↗

arXiv2015

Ecological collapse and the emergence of traveling waves at the onset of shear turbulence

The transition to turbulence exhibits remarkable spatio-temporal behavior that continues to defy detailed understanding. Near the onset to turbulence in pipes, transient turbulent regions decay either directly or, at higher Reynolds numbers through splitting, with characteristic time-scales that exhibit a super-exponential dependence on Reynolds number. Here we report numerical simulations of transitional pipe flow, showing that a zonal flow emerges at large scales, activated by anisotropic turbulent fluctuations; in turn, the zonal flow suppresses the small-scale turbulence leading to stochastic predator-prey dynamics. We show that this "ecological" model of transitional turbulence reproduces the super-exponential lifetime statistics and phenomenology of pipe flow experiments. Our work demonstrates that a fluid on the edge of turbulence is mathematically analogous to an ecosystem on the edge of extinction, and provides an unbroken link between the equations of fluid dynamics and the directed percolation universality class.

physics.flu-dyn↗

arXiv2014

Path integral calculation for emergence of rapid evolution from demographic stochasticity

Genetic variation in a population can sometimes arise so fast as to modify ecosystem dynamics. Such phenomena have been observed in natural predator-prey systems, and characterized in the laboratory as showing unusual phase relationships in population dynamics, including a $\pi$ phase shift between predator and prey (evolutionary cycles) and even undetectable prey oscillations compared to those of the predator (cryptic cycles). Here we present a generic individual-level stochastic model of interacting populations that includes a subpopulation of low nutritional value to the predator. Using a master equation formalism, and by mapping to a coherent state path integral solved by a system-size expansion, we show that evolutionary and cryptic quasicycles can emerge generically from the combination of intrinsic demographic fluctuations and clonal mutations alone, without additional biological mechanisms.

q-bio.PE↗

arXiv2011

Anomalous isotope effect in phonon-dressed iron-based superconductor

The role of electron-phonon interactions in iron-based superconductor is currently under debate with conflicting experimental reports on the isotope effect. To address this important issue, we employ the renormalization-group method to investigate the competition between electron-electron and electron-phonon interactions in these materials. The renormalization-group analysis shows that the ground state is a phonon-dressed unconventional superconductor: the dominant electronic interactions account for pairing mechanism while electron-phonon interactions are subdominant. Because of the phonon dressing, the isotope effect of the critical temperature can be normal or reversed, depending on whether the retarded intra- or inter-band interactions are altered upon isotope substitutions. The connection between the anomalous isotope effect and the unconventional pairing symmetry is discussed at the end.

cond-mat.supr-con↗

arXiv2011

Hierarchy of relevant couplings in perturbative renormalization group transformations

The phase diagram for the interacting fermions in weak coupling is described by the perturbative renormalization group equations. Due to the lack of analytic solutions for these coupled non-linear differential equations, it is rather subtle to tell which couplings are relevant or irrelevant. We propose a powerful classification scheme to build up the hierarchy of the relevant couplings by a scaling Ansatz found numerically. To demonstrate its superiority over the conventional classification for the relevant couplings, we apply this scheme to a controversial phase transition in the two-leg ladder and show that it should be a non-trivial crossover instead. The scaling Ansatz we propose here can classify the relevant couplings in hierarchical order without any ambiguity and can improve significantly how we interpret the numerical outcomes in general renormalization group methods.

cond-mat.str-el↗