arXiv subjects

Ran Ni

Publications and source records attributed to Ran Ni.

At least 19 recordsLinked to original sources

arXiv2026

Metastable Hyperuniformity at Discontinuous Absorbing Transitions

Nonequilibrium hyperuniformity can arise either as a steady-state property of driven active fluids or as a critical signature at continuous absorbing transition points in two and three dimensions. Whether analogous structural order exists near discontinuous absorbing transitions, and what mechanism generates it, remains unclear. Here, we show that discontinuous absorbing transitions generically host a metastable hyperuniform regime near the stability limit. Using a facilitated Manna model without center-of-mass conservation, we find anomalous scaling $S(k\to0)\sim k^{1.2}$, which appears only near the metastable regime and disappears both deep in the active phase and in the absorbing phase. This scaling is robust in both two and three dimensions, in contrast to critical hyperuniformity at continuous absorbing transitions. We further formulate a minimal conserved Reggeon field theory that reproduces the same metastable hyperuniform regime and anomalous scaling, demonstrating that the phenomenon does not rely on microscopic update rules but arises from the interplay of nonlinear activation, multiplicative demographic noise, and conserved diffusive fluctuations. These results identify metastable hyperuniformity as a generic pseudo-critical structural signature of discontinuous absorbing transitions coupled to a conserved density.

cond-mat.soft↗

arXiv2025

Entropy-driven physical amplification in multivalent biosensing

Sensitive detection of low-abundance molecular targets is widely assumed to require enzymatic amplification, such as PCR, to achieve low detection limits. In amplification-free platforms, sensitivity is traditionally constrained by equilibrium binding affinity. Here we show that multivalent linker entropy provides a distinct physical route to exponential sensitivity enhancement in purely equilibrium sensing architectures. Using a statistical-mechanical theory supported by grand canonical Monte Carlo simulations, we demonstrate that redistributing a fixed total interaction strength over increasing linker valency exponentially lowers adsorption thresholds. This scaling emerges not from stronger energetic affinity, but from the rapid growth of combinatorial binding configurations, revealing entropy as an intrinsic amplification mechanism. Consequently, detection limits can be tuned independently of bond strength, enabling ultrasensitive responses without enzymatic replication. Our results establish a general physical design principle for engineering amplification-free detection systems capable of approaching PCR-level sensitivities through entropy-driven collective effects.

cond-mat.soft↗

arXiv2025

A universal scaling law for active diffusion in complex media

Using granular experiments and computer simulations, we investigate the long-time diffusion of active tracers in a broad class of complex media composed of frozen obstacles of diverse structures. By introducing a dimensionless persistence length $Q = v_d \tau_r / d_t$, we propose a modified scaling relation that independently collapses experimental and simulation results across active and passive particles, diverse media, and distinct propulsion mechanisms. Our results reveal a universal active diffusion-structure relation that holds across both equilibrium and nonequilibrium regimes, providing a simple predictive framework for active diffusion in complex environments.

cond-mat.soft↗

arXiv2025

U-Net 3+ for Anomalous Diffusion Analysis enhanced with Mixture Estimates (U-AnD-ME) in particle-tracking data

Biophysical processes within living systems rely on encounters and interactions between molecules in complex environments such as cells. They are often described by anomalous diffusion transport. Recent advances in single-molecule microscopy and particle-tracking techniques have yielded an abundance of data in the form of videos and trajectories that contain critical information about these biologically significant processes. However, standard approaches for characterizing anomalous diffusion from these measurements often struggle in cases of practical interest, e.g. due to short, noisy trajectories. Fully exploiting this data therefore requires the development of advanced analysis methods -- a core goal at the heart of the recent international Anomalous Diffusion Challenges. Here, we introduce a novel machine-learning framework, U-net 3+ for Anomalous Diffusion analysis enhanced with Mixture Estimates (U-AnD-ME), that applies a U-Net 3+ based neural network alongside Gaussian mixture models to enable highly accurate characterisation of single-particle tracking data. In the 2024 Anomalous Diffusion Challenge, U-AnD-ME outperformed all other participating methods for the analysis of two-dimensional anomalous diffusion trajectories at both single-trajectory and ensemble levels. Using a large dataset inspired by the Challenge, we further characterize the performance of U-AnD-ME in segmenting trajectories and inferring anomalous diffusion properties.

physics.data-an↗

arXiv2024

Designed self-assembly of programmable colloidal atom-electron equivalents

To unlock the potential for assembling complex colloidal "molecules", we investigate a minimal binary system of programmable colloidal atom-electron equivalents (PAE-EE), where electron equivalents (EEs) are multivalent linkers with two distinct types of single-stranded DNA (ssDNA) ends complementary to those ssDNAs on binary programmable atom equivalents (PAEs). We derive a statistical mechanical framework for calculating the effective interaction between PAEs mediated by EEs with arbitrary valency, which quantitatively agrees with simulations that explicitly include EEs. Our analysis reveals an anomalous dependence of PAE-PAE interactions on the EE valency, showing that EE-mediated interactions converge at the large valency limit. Moreover, we identify an optimal EE valency that maximizes the interaction difference between targeted and non-targeted binding pairs of PAEs. These findings offer design principles for targeted self-assembly in PAE-EE systems.

cond-mat.soft↗

arXiv2024

Glass Transition in Monolayers of Rough Colloidal Ellipsoids

Structure-dynamics correlation is one of the major ongoing debates in the glass transition, although a number of structural features have been found connected to the dynamic heterogeneity in different glass-forming colloidal systems. Here using colloidal experiments combined with coarse-grained molecular dynamics simulations, we investigate the glass transition in monolayers of rough colloidal ellipsoids. Compared with smooth colloidal ellipsoids, the surface roughness of ellipsoids is found to significantly change the nature of glass transition. In particular, we find that the surface roughness induced by coating only a few small hemispheres on the ellipsoids can eliminate the existence of orientational glass and the two-step glass transition found in monolayers of smooth ellipsoids. This is due to the surface roughness-induced coupling between the translational and rotational degrees of freedom in colloidal ellipsoids, which also destroys the structure-dynamics correlation found in glass-forming suspensions of colloidal ellipsoids. Our results not only suggest a new way of using surface roughness to manipulate the glass transition in colloidal systems, but also highlight the importance of detailed particle shape on the glass transition and structure-dynamics correlation in suspensions of anisotropic colloids.

cond-mat.soft↗

arXiv2024

Non-equilibrium dynamic hyperuniform states

Disordered hyperuniform structures are an exotic state of matter having suppressed density fluctuations at large length-scale similar to perfect crystals and quasicrystals but without any long range orientational order. In the past decade, an increasing number of non-equilibrium systems were found to have dynamic hyperuniform states, which have emerged as a new research direction coupling both non-equilibrium physics and hyperuniformity. Here we review the recent progress in understanding dynamic hyperuniform states found in various non-equilibrium systems, including the critical hyperuniformity in absorbing phase transitions, non-equilibrium hyperuniform fluids and the hyperuniform structures in phase separating systems via spinodal decomposition.

cond-mat.soft↗

arXiv2024

Efficient Rare Event Sampling with Unsupervised Normalising Flows

From Physics and Biology to Seismology and Economics, the behaviour of countless systems is determined by impactful yet unlikely transitions between metastable states known as \emph{rare events}, the study of which is essential for understanding and controlling these systems' properties. Classical computational methods to sample rare events remain prohibitively inefficient, and are a bottleneck for enhanced samplers requiring prior data. Here, we introduce a novel framework, FlowRES that uses unsupervised normalising flow neural networks to enhance Monte Carlo sampling of rare events by generating high-quality nonlocal Monte Carlo proposals. We validate FlowRES by sampling the transition path ensembles of equilibrium and non-equilibrium systems of Brownian particles exploring increasingly complex potential surfaces. Beyond eliminating requirements for prior data, FlowRES features key advantages over established samplers: no collective variables need defining, its efficiency remains constant even as events become increasingly unlikely, and it can handle systems with multiple routes between states.

physics.comp-ph↗

arXiv2023

Quantitative evaluation of methods to analyze motion changes in single-particle experiments

The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the particle trajectories. Despite the existence of multiple approaches to carry out this type of analysis, no objective assessment of these methods has been performed so far. Here, we report the results of a competition to characterize and rank the performance of these methods when analyzing the dynamic behavior of single molecules. To run this competition, we implemented a software library that simulates realistic data corresponding to widespread diffusion and interaction models, both in the form of trajectories and videos obtained in typical experimental conditions. The competition constitutes the first assessment of these methods, providing insights into the current limitations of the field, fostering the development of new approaches, and guiding researchers to identify optimal tools for analyzing their experiments.

cond-mat.soft↗

arXiv2023

A bond swap algorithm for simulating dynamically crosslinked polymers

Materials incorporating covalent adaptive networks (CAN), e.g., vitrimers, have received significant scientific attention due to their distinctive attributes of self-healing and stimuli-responsive properties. Different from direct crosslinked systems, bivalent and multivalent systems require a bond swap algorithm that respects detailed balance, considering the multiple equilibria in the system. Here we propose a simple and robust algorithm to handle bond swap in multivalent and multi-species CAN systems. By including a bias term in the acceptance of Monte Carlo moves, we eliminate the imbalance from the bond swap site selection and multivalency effects, ensuring the detailed balance for all species in the system.

cond-mat.soft↗

arXiv2023

Designing superselectivity in linker-mediated multivalent nanoparticle adsorption

Using a statistical mechanical model and numerical simulations, we provide the design principle for the bridging strength ($\xi$) and linker density ($\rho$) dependent superselectivity in linker-mediated multivalent nanoparticle adsorption. When the bridges are insufficient, the formation of multiple bridges leads to both $\xi$- and $\rho$-dependent superselectivity. Whereas, when the bridges are excessive, the system becomes insensitive to bridging strength due to entropy-induced self-saturation and shows a superselective desorption with respect to the linker density. Counterintuitively, lower linker density or stronger bridging strength enhances the superselectivity. These findings enhance understanding of relevant biological processes and open up opportunities for applications in biosensing, drug delivery, and programmable self-assembly.

cond-mat.soft↗

arXiv2023

Optimal face-to-face coupling for fast self-folding kirigami

Kirigami-inspired designs can enable self-folding three-dimensional materials from flat, two-dimensional sheets. Hierarchical designs of connected levels increase the diversity of possible target structures, yet they can lead to longer folding times in the presence of fluctuations. Here, we study the effect of rotational coupling between levels on the self-folding of two-level kirigami designs driven by thermal noise in a fluid. Naturally present due to hydrodynamic resistance, we find that optimization of this coupling as control parameter can significantly improve a structure's self-folding rate and yield.

cond-mat.soft↗

arXiv2023

How does a hyperuniform fluid freeze?

All phase transitions can be categorised into two different types: continuous and discontinuous phase transitions. Discontinuous phase transitions are normally accompanied with significant structural changes, and nearly all of them have the kinetic pathway of nucleation and growth, if the system does not suffer from glassy dynamics. Here, in a system of barrier-controlled reactive particles, we find that the discontinuous freezing transition of a non-equilibrium hyperuniform fluid into an absorbing state does not have the kinetic pathway of nucleation and growth, and the transition is triggered by long wavelength fluctuations. The transition rate decreases with increasing the system size, which suggests that the metastable hyperuniform fluid is kinetically stable in an infinitely large system. This challenges the common understanding of metastability in discontinuous phase transitions. Moreover, we find that the ``metastable yet kinetically stable'' hyperuniform fluid features a new scaling in the structure factor $S(k \rightarrow 0) \sim k^{1.2}$ in 2D, which is the third dynamic hyperuniform state in addition to the critical hyperuniform state with $S(k \rightarrow 0) \sim k^{0.45}$ and the non-equilibrium hyperuniform fluid with $S(k \rightarrow 0) \sim k^{2}$.

cond-mat.soft↗

arXiv2023

Random organization and non-equilibrium hyperuniform fluids on a sphere

Random organizing hyperuniform fluid induced by reciprocal activation is a non-equilibrium fluid with vanishing density fluctuations at large length scales like crystals. Here we extend this new state of matter to a closed manifold, namely a spherical surface. We find that the random organization on a spherical surface behaves similar to that in two dimensional Euclidean space, and the absorbing transition on a sphere also belongs to the conserved directed percolation universality class. Moreover, the reciprocal activation can also induce a non-equilibrium hyperuniform fluid on a sphere. The spherical structure factor at the absorbing transition and the non-equilibrium hyperuniform fluid phases are scaled as $S(l \rightarrow 0) \sim (l/R)^{0.45}$ and $S(l \rightarrow 0) \sim l(l+1)/R^2$, respectively, which are both hyperuniform according to the definition of hyperuniformity on a sphere with $l$ the wave number and $R$ the radius of the spherical surface. We also consider the impact of inertia in realistic hyperuniform fluids, and it is found only adding an extra length-scale, above which hyperuniform scaling appears. Our finding suggests a new method for creating non-equilibrium hyperuniform fluids on closed manifolds to avoid boundary effects.

cond-mat.soft↗

arXiv2022

The role of receptor uniformity in multivalent binding

Multivalency is prevalent in various biological systems and applications due to the superselectivity that arises from the cooperativity of multivalent binding. Traditionally, it was thought that weaker individual binding would improve the selectivity in multivalent targeting. Here using analytical mean field theory and Monte Carlo simulations, we discover that for receptors that are highly uniformly distributed, the highest selectivity occurs at an intermediate binding energy and can be significantly greater than the weak binding limit. This is caused by an exponential relationship between the bound fraction and receptor concentration, which is influenced by both the strength and combinatorial entropy of binding. Our findings not only provide new guidelines for the rational design of biosensors using multivalent nano-particles but also introduce a new perspective in understanding biological processes involving multivalency.

cond-mat.soft↗

arXiv2022

Interplay between jamming and MIPS in persistent self-propelling particles

In living and engineered systems of active particles, self-propulsion induces an unjamming transition from a solid to a fluid phase and phase separation between a gas and a liquid-like phase. We demonstrate an interplay between these two nonequilibrium transitions in systems of persistent active particles. The coexistence and jamming lines in the activity-density plane meet at the jamming transition point in the limit of hard particles or zero activity. This interplay induces an anomalous dynamic in the liquid phase and hysteresis at the active jamming transition.

cond-mat.soft↗

arXiv2022

Comment on "Explicit Analytical Solution for Random Close Packing in $d=2$ and $d=3$"

In this short commentary we provide our comment on the article "Explicit Analytical Solution for Random Close Packing in $d=2$ and $d=3$" and its subsequent Erratum that are recently published in Physical Review Letters. In that Letter, the author presented an explicit analytical derivation of the volume fractions $\phi_{\rm RCP}$ for random close packings (RCP) in both $d=2$ and $d=3$. Here we first briefly show the key parts of the derivation in Ref.~\cite{Za22}, and then provide arguments on why we think the derivation of the analytical results is problematic and unjustified, and why the Erratum does not address or clarify the concerns raised previously by us.

cond-mat.soft↗

arXiv2022

Entropy driven thermo-gelling vitrimer

Thermo-gelling polymers have been envisioned as promising smart biomaterials but limited to their weak mechanical and thermodynamic stabilities. Here we propose a new thermo-gelling vitrimer, which remains at a liquid state because of the addition of protector molecules preventing the crosslinking, and with increasing temperature, an entropy driven crosslinking occurs to induce the sol-gel transition. Moreover, we find that the activation barrier in the metathesis reaction of vitrimers plays an important role, and experimentally one can use catalysts to tune the activation barrier to drive the vitrimer to form an equilibrium gel at high temperature, which is not subject to any thermodynamic instability. We formulate a mean field theory to describe the entropy driven crosslinking of the vitrimer, which agrees quantitatively with computer simulations, and paves the way for design and fabrication of novel vitrimers for biomedical applications.

cond-mat.soft↗