arXiv subjects

Wencheng Ji

Publications and source records attributed to Wencheng Ji.

14 recordsLinked to original sources

arXiv2025

Design principles of transcription factors with intrinsically disordered regions

Transcription Factors (TFs) are proteins crucial for regulating gene expression. Effective regulation requires the TFs to rapidly bind to their correct target, enabling the cell to respond efficiently to stimuli such as nutrient availability or the presence of toxins. However, the search process is hindered by slow diffusive movement and the presence of `false' targets --DNA segments that are similar to the true target. In eukaryotic cells, most TFs contain an Intrinsically Disordered Region (IDR), which is commonly assumed to behave as a long, flexible polymeric tail composed of hundreds of amino acids. Recent experimental findings indicate that the IDR of certain TFs plays a pivotal role in the search process. However, the principles underlying the IDR's role remain unclear. Here, we reveal key design principles of the IDR related to TF binding affinity and search time. Our results demonstrate that the IDR significantly enhances both of these aspects. Furthermore, our model shows good agreement with experimental results, and we propose further experiments to validate the model's predictions.

physics.bio-ph↗

arXiv2025

Disentangling hierarchical relaxations in glass formers via dynamic eigenmodes

Hierarchical dynamics in glass-forming systems span multiple timescales, from fast vibrations to slow structural rearrangements, appearing in both supercooled fluids and glassy states. Understanding how these diverse processes interact across timescales remains a central challenge. Here, by combining direct particle-level observations with a dynamic eigenmode approach that decomposes intermediate-timescale responses into distinct modes, we reveal the microscopic organisation of relaxation dynamics in two-dimensional colloidal systems. We identify five classes of modes characterizing hierarchical dynamics: (i) quasi-elastic modes, (ii) slow-reversible string modes contributing to dynamic heterogeneity, (iii) slow-irreversible string modes leading to flow, (iv) fast-$β$ modes with fast-reversible strings, and (v) random noise modes. The emergence of quasi-elastic modes marks the onset of glassy dynamics, while reversible string modes dominate dynamic heterogeneity throughout both supercooled and glassy regimes. Our findings offer a unified microscopic framework for understanding how distinct relaxation processes interconnect across timescales, illuminating the mechanisms driving glass formation.

cond-mat.soft↗

arXiv2024

The Role of Excitations in Supercooled Liquids: Density, Geometry, and Relaxation Dynamics

Low-energy excitations play a key role in all condensed-matter systems, yet there is limited understanding of their nature in glasses, where they correspond to local rearrangements of groups of particles. Here we introduce an algorithm to systematically uncover these excitations up to the activation energy scale relevant to structural relaxation. We use it in a model system to measure the density of states on a scale never achieved before, confirming that this quantity shifts to higher energy under cooling, precisely as the activation energy does. Secondly, we show that the excitations' energetic and spatial features allow one to predict with great accuracy the dynamic propensity, i.e. the location of future relaxation dynamics. Finally, we find that excitations have a core whose properties, including the displacement of the most mobile particle, scale as a power-law of their activation energy and are independent of temperature. Additionally, they exhibit an outer deformation field that depends on the material's stability and, therefore, on temperature. We build a scaling description of these findings. Overall, our analysis supports that excitations play a crucial role in regulating relaxation dynamics near the glass transition, effectively suppressing the transition to dynamical arrest predicted by mean-field theories while also being strongly influenced by it.

cond-mat.soft↗

arXiv2024

Local vs. Cooperative: Unraveling Glass Transition Mechanisms with SEER

Which phenomenon slows down the dynamics in super-cooled liquids and turns them into glasses is a long-standing question of condensed-matter. Most popular theories posit that as the temperature decreases, many events must occur in a coordinated fashion on a growing length scale for relaxation to occur. Instead, other approaches consider that local barriers associated with the elementary rearrangement of a few particles or `excitations' govern the dynamics. To resolve this conundrum, our central result is to introduce an algorithm, SEER, which can systematically extract hundreds of excitations and their energy from any given configuration. We also provide a novel measurement of the activation energy, characterizing the liquid dynamics, based on fast quenching and reheating. We use these two methods in a popular liquid model of polydisperse particles. Such polydisperse models are known to capture the hallmarks of the glass transition and can be equilibrated efficiently up to millisecond time scales. The analysis reveals that cooperative effects do not control the fragility of such liquids: the change of energy of local barriers determines the change of activation energy. More generally, these methods can now be used to measure the degree of cooperativity of any liquid model.

cond-mat.soft↗

arXiv2022

Scaling description of creep flow in amorphous solids

Amorphous solids such as coffee foam, toothpaste or mayonnaise display a transient creep flow when a stress $Σ$ is suddenly imposed. The associated strain rate is commonly found to decay in time as $\dotγ \sim t^{-ν}$, followed either by arrest or by a sudden fluidisation. Various empirical laws have been suggested for the creep exponent $ν$ and fluidisation time $τ_f$ in experimental and numerical studies. Here, we postulate that plastic flow is governed by the difference between $Σ$ and the transient yield stress $Σ_t(γ)$ that characterises the stability of configurations visited by the system at strain $γ$. Assuming the analyticity of $Σ_t(γ)$ allows us to predict $ν$ and asymptotic behaviours of $τ_f$ in terms of properties of stationary flows. We test successfully our predictions using elastoplastic models and published experimental results.

cond-mat.soft↗

arXiv2022

Mean-field description for the architecture of low-energy excitations in glasses

In amorphous materials, groups of particles can rearrange locally into a new stable configuration. Such elementary excitations are key as they determine the response to external stresses, as well as to thermal and quantum fluctuations. Yet, understanding what controls their geometry remains a challenge. Here we build a scaling description of the geometry and energy of low-energy excitations in terms of the distance to an instability, as predicted for instance at the dynamical transition in mean field approaches of supercooled liquids. We successfully test our predictions in ultrastable computer glasses, with a gapped and ungapped (regular) spectrum. Overall, our approach explains why excitations become less extended, with a higher energy and displacement scale upon cooling.

cond-mat.soft↗

arXiv2021

Toward understanding the depletion of two-level systems in ultrastable glasses

The density of Two-level systems (TLS) controls the low-temperature thermal properties in glasses and has been found to be almost depleted in ultrastable glasses. While this depletion of TLS is thought to have a close relationship with the dramatic decrease of quasi-localized modes (QLMs), it has yet to be clearly formalized. In this work, we argue, based on the \textit{soft-potential} model, that TLS correspond to QLMs with typical frequency $ω_0$. The density $n_0$ of TLS is proportional to both the density of QLMs $D_L(ω_0)$, and the fraction of symmetric double-wells $f(ω_0)$ at $ω_0$, i.e., $n_0 \propto D_L(ω_0)f(ω_0)$. We numerically estimate $ω_0$ and $n_0$ in computer glasses at different levels of stabilities, and find that $ω_0$ is about $5\%$ to $10\%$ of the Debye frequency. $n_0$ in ultrastable glasses is over $1000$ times smaller than that in poorly prepared glasses, with both $D_L(ω_0)$ and $f(ω_0)$ decreasing significantly. Remarkably, the order of magnitude of estimations for $n_0$ agrees with that found in experiments in amorphous silicon. Our study paves the way to understanding the depletion of TLS through the rarefaction of QLMs.

cond-mat.dis-nn↗

arXiv2020

Thermal origin of quasi-localised excitations in glasses

Key aspects of glasses are controlled by the presence of excitations in which a group of particles can rearrange. Surprisingly, recent observations indicate that their density is dramatically reduced and their size decreases as the temperature of the supercooled liquid is lowered. Some theories predict these excitations to cause a gap in the spectrum of quasi-localised modes of the Hessian that grows upon cooling, while others predict a pseudo-gap ${D_L(ω)} \sim ω^α$. To unify these views and observations, we generate glassy configurations of controlled gap magnitude $ω_c$ at temperature ${T=0}$, using so-called `breathing' particles, and study how such gapped states respond to thermal fluctuations. We find that \textit{(i)}~the gap always fills up at finite $T$ with ${D_L(ω) \approx A_4(T) \, ω^4}$ and ${A_4 \sim \exp(-E_a / T)}$ at low $T$, \textit{(ii)}~$E_a$ rapidly grows with $ω_c$, in reasonable agreement with a simple scaling prediction ${E_a\sim ω_c^4}$ and \textit{(iii)}~at larger $ω_c$ excitations involve fewer particles, as we rationalise, and eventually become string-like. We propose an interpretation of mean-field theories of the glass transition, in which the modes beyond the gap act as an excitation reservoir, from which a pseudo-gap distribution is populated with its magnitude rapidly decreasing at lower $T$. We discuss how this picture unifies the rarefaction as well as the decreasing size of excitations upon cooling, together with a string-like relaxation occurring near the glass transition.

cond-mat.soft↗

arXiv2020

Thermally activated flow in models of amorphous solids

Amorphous solids yield at a critical value $Σ_c$ of the imposed stress $Σ$ through a dynamical phase transition. While sharp in athermal systems, the presence of thermal fluctuations leads to the rounding of the transition and thermally activated flow even below $Σ_c$. Here, we study the steady state thermal flow of amorphous solids using a mesoscopic elasto-plastic model. In the Hebraud-Lequex (HL) model we provide an analytical solution of the thermally activated flow at low temperature. We then propose a general scaling law that also describes the transition rounding. Finally, we find that the scaling law holds in numerical simulations of the HL model, a 2D elasto-plastic model, and in previously published molecular dynamics simulations of 2D Lennard-Jones glass.

cond-mat.soft↗

arXiv2019

How collective asperity detachments nucleate slip at frictional interfaces

Sliding at a quasi-statically loaded frictional interface can occur via macroscopic slip events, which nucleate locally before propagating as rupture fronts very similar to fracture. We introduce a novel microscopic model of a frictional interface that includes asperity-level disorder, elastic interaction between local slip events, and inertia. For a perfectly flat and homogeneously loaded interface, we find that slip is nucleated by avalanches of asperity detachments of extension larger than a critical radius $A_c$ governed by a Griffith criterion. We find that after slip, the density of asperities at a local distance to yielding $x_σ$ presents a pseudo-gap $P(x_σ) \sim (x_σ)^θ$, where $θ$ is a non-universal exponent that depends on the statistics of the disorder. This result makes a link between friction and the plasticity of amorphous materials where a pseudo-gap is also present. For friction, we find that a consequence is that stick-slip is an extremely slowly decaying finite size effect, while the slip nucleation radius $A_c$ diverges as a $θ$-dependent power law of the system size. We discuss how these predictions can be tested experimentally.

cond-mat.dis-nn↗

arXiv2019

Theory for the density of interacting quasi-localised modes in amorphous solids

Quasi-localised modes appear in the vibrational spectrum of amorphous solids at low-frequency. Though never formalised, these modes are believed to have a close relationship with other important local excitations, including shear transformations and two-level systems. We provide a theory for their frequency density, $D_{L}(ω)\simω^α$, that establishes this link for systems at zero temperature under quasi-static loading. It predicts two regimes depending on the density of shear transformations $P(x)\sim x^θ$ (with $x$ the additional stress needed to trigger a shear transformation). If $θ>1/4$, $α=4$ and a finite fraction of quasi-localised modes form shear transformations, whose amplitudes vanish at low frequencies. If $θ<1/4$, $α=3+ 4 θ$ and all quasi-localised modes form shear transformations with a finite amplitude at vanishing frequencies. We confirm our predictions numerically.

cond-mat.soft↗

arXiv2019

Fast generation of ultrastable computer glasses by minimization of an augmented potential energy

We present a model and protocol that enable the generation of extremely stable computer glasses at minimal computational cost. The protocol consists of an instantaneous quench in an augmented potential energy landscape, with particle radii as additional degrees of freedom. We demonstrate how our glasses' mechanical stability, which is readily tunable in our approach, is reflected both in microscopic and macroscopic observables. Our observations indicate that the stability of our computer glasses is at least comparable to that of computer glasses generated by the celebrated Swap Monte Carlo algorithm. Strikingly, some key properties support even qualitatively enhanced stability in our scheme: the density of quasilocalized excitations displays a gap in our most stable computer glasses, whose magnitude scales with the polydispersity of the particles. We explain this observation, which is consistent with the lack of plasticity we observe at small stress. It also suggests that these glasses are depleted from two-level systems, similarly to experimental vapor-deposited ultrastable glasses.

cond-mat.soft↗

arXiv2017

Dynamics of the Wigner Crystal of Composite Particles

Conventional wisdom had long held that a composite particle behaves just like an ordinary Newtonian particle. In this paper, we derive the effective dynamics of a type-I Wigner crystal of composite particles directly from its microscopic wave function. It indicates that the composite particles are subjected to a Berry curvature in the momentum space as well as an emergent dissipationless viscosity. Therefore, contrary to the general belief, composite particles follow the more general Sundaram-Niu dynamics instead of the ordinary Newtonian one. We show that the presence of the Berry curvature is an inevitable feature for a dynamics consistent with the dipole picture of composite particles and Kohn's theorem. Based on the dynamics, we determine the dispersions of magneto-phonon excitations numerically. We find an emergent magneto-roton mode which signifies the composite-particle nature of the Wigner crystal. It occurs at frequencies much lower than the magnetic cyclotron frequency and has a vanishing oscillator strength in the long wavelength limit.

cond-mat.str-el↗

arXiv2016

Topological Phonon Modes in A Two-Dimensional Wigner Crystal

We investigate the spin-orbit coupling effect in a two-dimensional Wigner crystal. We show that sufficiently strong spin-orbit coupling and an appropriate sign of g-factor could transform the Wigner crystal to a topological phonon system. We demonstrate the existence of chiral phonon edge modes in finite size samples, as well as the robustness of the modes in the topological phase. We explore the possibility of realizing the topological phonon system in two-dimensional Wigner crystals confined in semiconductor quantum wells/heterostructure. We find that the spin-orbit coupling is too weak for driving a topological phase transition in these systems. We argue that one may look for the topological phonon system in correlated Wigner crystals with emergent effective spin-orbit coupling.

cond-mat.mes-hall↗