# Browsing by Author "Hu, Yi"

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Item Open Access Application of area scaling analysis to identify natural killer cell and monocyte involvement in the GranToxiLux antibody dependent cell-mediated cytotoxicity assay.(Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2018-04) Pollara, Justin; Orlandi, Chiara; Beck, Charles; Edwards, R Whitney; Hu, Yi; Liu, Shuying; Wang, Shixia; Koup, Richard A; Denny, Thomas N; Lu, Shan; Tomaras, Georgia D; DeVico, Anthony; Lewis, George K; Ferrari, GuidoSeveral different assay methodologies have been described for the evaluation of HIV or SIV-specific antibody-dependent cell-mediated cytotoxicity (ADCC). Commonly used assays measure ADCC by evaluating effector cell functions, or by detecting elimination of target cells. Signaling through Fc receptors, cellular activation, cytotoxic granule exocytosis, or accumulation of cytolytic and immune signaling factors have been used to evaluate ADCC at the level of the effector cells. Alternatively, assays that measure killing or loss of target cells provide a direct assessment of the specific killing activity of antibodies capable of ADCC. Thus, each of these two distinct types of assays provides information on only one of the critical components of an ADCC event; either the effector cells involved, or the resulting effect on the target cell. We have developed a simple modification of our previously described high-throughput ADCC GranToxiLux (GTL) assay that uses area scaling analysis (ASA) to facilitate simultaneous quantification of ADCC activity at the target cell level, and assessment of the contribution of natural killer cells and monocytes to the total observed ADCC activity when whole human peripheral blood mononuclear cells are used as a source of effector cells. The modified analysis method requires no additional reagents and can, therefore, be easily included in prospective studies. Moreover, ASA can also often be applied to pre-existing ADCC-GTL datasets. Thus, incorporation of ASA to the ADCC-GTL assay provides an ancillary assessment of the ability of natural and vaccine-induced antibodies to recruit natural killer cells as well as monocytes against HIV or SIV; or to any other field of research for which this assay is applied. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of ISAC.Item Open Access Caging and Transport in Simple Disordered Systems(2021) Hu, YiRecent advances on the glass problem motivate reexamining classical models of caging and transport. In particular, seemingly incompatible percolation and mean-field caging descriptions on the localization transition call for better understanding both. In light of this fundamental inconsistency, we study the caging and transport of a series of simple disordered systems.

We first consider the dynamics of site percolation on hypercubic lattices. Using theory and simulations, we obtain that both caging and subdiffusion scale logarithmically for dimension d ≥ d_u, the upper critical dimension of percolation. The theoretical derivation on Bethe lattice and a random graph confirm that logarithmic scalings should persist in the limit d→∞. The computational validation evaluates directly the dynamical critical exponents below d_u as well as their logarithmic scaling above d_u. Our numerical results improve various earlier estimates and are fully consistent with our theoretical predictions.

Recent implementation of efficient simulation algorithms for high-dimensional systems also facilitates the study of dense packing lattices beyond the conventional hypercubic ones. Here, we consider the percolation problem on checkerboard D_d lattices and on E_8 relatives for d=6 to 9. Precise estimates for both site and bond percolation thresholds obtained from invasion percolation simulations are compared with dimensional series expansion based on lattice animal enumeration for D_d lattices. As expected, the bond percolation threshold rapidly approaches the Bethe lattice limit as d increases for these high-connectivity lattices. Corrections, however, exhibit clear yet unexplained trends.

The random Lorentz gas (RLG) is a minimal model for transport in disordered media. Despite the broad relevance of the model, theoretical grasp over its properties remains weak. Here, we first extend analytical expectations for asymptotic high-d bounds on the void percolation threshold, and then computationally evaluate both the threshold and its criticality in various d. A simple modification of the RLG is found to bring the mean-field-like caging down to d=3.

The RLG also provides a toy model of particle caging, which is known to be relevant for describing the discontinuous dynamical transition of glasses. Following the percolation studies, we consider its exact mean-field solution in the d→∞ limit and perform simulation in d=2...20. We find that for sufficiently high d the mean-field caging transition precedes and prevents the percolation transition, which only happens on timescales diverging with d. This perturbative correction is associated with the cage heterogeneity. We further show that activated processes related to rare cage escapes destroy the glass transition in finite dimensions, leading to a rich interplay between glassiness and percolation physics. This advance suggests that the RLG can be used as a toy model to develop a first-principle description of particle hopping in structural glasses.

While the cages in the RLG are formed by non-interacting obstacles, cage structure is important for the hopping process in three-dimensional glasses. As a final note and also a future direction, a study on the three-dimensional polydisperse hard spheres with modification, named as the Mari-Kurchan-Krzakala (MKK) model was proposed. This consideration provides a controllable way to interpolate between the mean-field and the real space glasses. These insights help chart a path toward a complete description of finite-dimensional glasses.

Item Open Access Clustering and assembly dynamics of a one-dimensional microphase former.(Soft matter, 2018-03-26) Hu, Yi; Charbonneau, PatrickBoth ordered and disordered microphases ubiquitously form in suspensions of particles that interact through competing short-range attraction and long-range repulsion (SALR). While ordered microphases are more appealing materials targets, understanding the rich structural and dynamical properties of their disordered counterparts is essential to controlling their mesoscale assembly. Here, we study the disordered regime of a one-dimensional (1D) SALR model, whose simplicity enables detailed analysis by transfer matrices and Monte Carlo simulations. We first characterize the signature of the clustering process on macroscopic observables, and then assess the equilibration dynamics of various simulation algorithms. We notably find that cluster moves markedly accelerate the mixing time, but that event chains are of limited help in the clustering regime. These insights will inspire further study of three-dimensional microphase formers.Item Open Access Dynamics around the Site Percolation Threshold on High-Dimensional Hypercubic LatticesBiroli, Giulio; Charbonneau, Patrick; Hu, YiRecent advances on the glass problem motivate reexamining classical models of percolation. Here, we consider the displacement of an ant in a labyrinth near the percolation threshold on cubic lattices both below and above the upper critical dimension of simple percolation, d_u=6. Using theory and simulations, we consider the scaling regime part, and obtain that both caging and subdiffusion scale logarithmically for d >= d_u. The theoretical derivation considers Bethe lattices with generalized connectivity and a random graph model, and employs a scaling analysis to confirm that logarithmic scalings should persist in the infinite dimension limit. The computational validation employs accelerated random walk simulations with a transfer-matrix description of diffusion to evaluate directly the dynamical critical exponents below d_u as well as their logarithmic scaling above d_u. Our numerical results improve various earlier estimates and are fully consistent with our theoretical predictions.Item Open Access Equilibrium fluctuations in mean-field disordered models.(Physical review. E, 2022-08) Folena, Giampaolo; Biroli, Giulio; Charbonneau, Patrick; Hu, Yi; Zamponi, FrancescoMean-field models of glasses that present a random first order transition exhibit highly nontrivial fluctuations. Building on previous studies that focused on the critical scaling regime, we here obtain a fully quantitative framework for all equilibrium conditions. By means of the replica method we evaluate Gaussian fluctuations of the overlaps around the thermodynamic limit, decomposing them in thermal fluctuations inside each state and heterogeneous fluctuations between different states. We first test and compare our analytical results with numerical simulation results for the p-spin spherical model and the random orthogonal model, and then analyze the random Lorentz gas. In all cases, a strong quantitative agreement is obtained. Our analysis thus provides a robust scheme for identifying the key finite-size (or finite-dimensional) corrections to the mean-field treatment of these paradigmatic glass models.Item Open Access High-dimensional percolation criticality and hints of mean-field-like caging of the random Lorentz gas.(Physical review. E, 2021-08) Charbonneau, Benoit; Charbonneau, Patrick; Hu, Yi; Yang, ZhenThe random Lorentz gas (RLG) is a minimal model for transport in disordered media. Despite the broad relevance of the model, theoretical grasp over its properties remains weak. For instance, the scaling with dimension d of its localization transition at the void percolation threshold is not well controlled analytically nor computationally. A recent study [Biroli et al., Phys. Rev. E 103, L030104 (2021)2470-004510.1103/PhysRevE.103.L030104] of the caging behavior of the RLG motivated by the mean-field theory of glasses has uncovered physical inconsistencies in that scaling that heighten the need for guidance. Here we first extend analytical expectations for asymptotic high-d bounds on the void percolation threshold and then computationally evaluate both the threshold and its criticality in various d. In high-d systems, we observe that the standard percolation physics is complemented by a dynamical slowdown of the tracer dynamics reminiscent of mean-field caging. A simple modification of the RLG is found to bring the interplay between percolation and mean-field-like caging down to d=3.Item Open Access Interplay between percolation and glassiness in the random Lorentz gas.(Physical review. E, 2021-03) Biroli, Giulio; Charbonneau, Patrick; Corwin, Eric I; Hu, Yi; Ikeda, Harukuni; Szamel, Grzegorz; Zamponi, FrancescoThe random Lorentz gas (RLG) is a minimal model of transport in heterogeneous media that exhibits a continuous localization transition controlled by void space percolation. The RLG also provides a toy model of particle caging, which is known to be relevant for describing the discontinuous dynamical transition of glasses. In order to clarify the interplay between the seemingly incompatible percolation and caging descriptions of the RLG, we consider its exact mean-field solution in the infinite-dimensional d→∞ limit and perform numerics in d=2...20. We find that for sufficiently high d the mean-field caging transition precedes and prevents the percolation transition, which only happens on timescales diverging with d. We further show that activated processes related to rare cage escapes destroy the glass transition in finite dimensions, leading to a rich interplay between glassiness and percolation physics. This advance suggests that the RLG can be used as a toy model to develop a first-principle description of particle hopping in structural glasses.Item Open Access Local dynamical heterogeneity in glass formers(2021-09-24) Biroli, Giulio; Charbonneau, Patrick; Folena, Giampaolo; Hu, Yi; Zamponi, FrancescoWe study the local dynamical fluctuations in glass-forming models of particles embedded in $d$-dimensional space, in the mean-field limit of $d\to\infty$. Our analytical calculation reveals that single-particle observables, such as squared particle displacements, display divergent fluctuations around the dynamical (or mode-coupling) transition, due to the emergence of nontrivial correlations between displacements along different directions. This effect notably gives rise to a divergent non-Gaussian parameter, $\alpha_2$. The $d\to\infty$ local dynamics therefore becomes quite rich upon approaching the glass transition. The finite-$d$ remnant of this phenomenon further provides a long sought-after, first-principle explanation for the growth of $\alpha_2$ around the glass transition that is \emph{not based on multi-particle correlations}.Item Open Access Local Dynamical Heterogeneity in Simple Glass Formers.(Physical review letters, 2022-04) Biroli, Giulio; Charbonneau, Patrick; Folena, Giampaolo; Hu, Yi; Zamponi, FrancescoWe study the local dynamical fluctuations in glass-forming models of particles embedded in d-dimensional space, in the mean-field limit of d→∞. Our analytical calculation reveals that single-particle observables, such as squared particle displacements, display divergent fluctuations around the dynamical (or mode-coupling) transition, due to the emergence of nontrivial correlations between displacements along different directions. This effect notably gives rise to a divergent non-Gaussian parameter, α_{2}. The d→∞ local dynamics therefore becomes quite rich upon approaching the glass transition. The finite-d remnant of this phenomenon further provides a long sought-after, first-principle explanation for the growth of α_{2} around the glass transition that is not based on multiparticle correlations.Item Open Access Mean-Field Caging in a Random Lorentz Gas.(The journal of physical chemistry. B, 2021-06-07) Biroli, Giulio; Charbonneau, Patrick; Hu, Yi; Ikeda, Harukuni; Szamel, Grzegorz; Zamponi, FrancescoThe random Lorentz gas (RLG) is a minimal model of both percolation and glassiness, which leads to a paradox in the infinite-dimensional,*d*→ ∞ limit: the localization transition is then expected to be*continuous*for the former and*discontinuous*for the latter. As a putative resolution, we have recently suggested that, as*d*increases, the behavior of the RLG converges to the glassy description and that percolation physics is recovered thanks to finite-*d*perturbative and nonperturbative (instantonic) corrections [Biroli et al.*Phys. Rev. E*2021, 103, L030104]. Here, we expand on the*d*→ ∞ physics by considering a simpler static solution as well as the dynamical solution of the RLG. Comparing the 1/*d*correction of this solution with numerical results reveals that even perturbative corrections fall out of reach of existing theoretical descriptions. Comparing the dynamical solution with the mode-coupling theory (MCT) results further reveals that, although key quantitative features of MCT are far off the mark, it does properly capture the discontinuous nature of the*d*→ ∞ RLG. These insights help chart a path toward a complete description of finite-dimensional glasses.Item Open Access Morphology of renormalization-group flow for the de Almeida-Thouless-Gardner universality classCharbonneau, Patrick; Hu, Yi; Raju, Archishman; Sethna, James P; Yaida, ShoA replica-symmetry-breaking phase transition is predicted in a host of disordered media. The criticality of the transition has, however, long been questioned below its upper critical dimension, six, due to the absence of a critical fixed point in the renormalization-group flows at one-loop order. A recent two-loop analysis revealed a possible strong-coupling fixed point but, given the uncontrolled nature of perturbative analysis in the strong-coupling regime, debate persists. Here we examine the nature of the transition as a function of spatial dimension and show that the strong-coupling fixed point can go through a Hopf bifurcation, resulting in a critical limit cycle and a concomitant discrete scale invariance. We further investigate a different renormalization scheme and argue that the basin of attraction of the strong-coupling fixed point/limit cycle may thus stay finite for all dimensions.Item Open Access Numerical Transfer Matrix Method of Next-nearest-neighbor Ising Models(2021) Hu, YiIn statistical physics, the exact partition function of simple (quasi)-one-dimensional models can be obtained from the numerical transfer matrix (TM) method. This method involves solving for the leading eigenvalues of a matrix representing all possible interactions between the states that a unit of the system can take. Because the size of this matrix grows exponentially with the number of those units, the TM method is ideally suited for models that have a finite state space and short-range interactions. Its success nevertheless relies on the use of efficient iterative eigensolvers and on leveraging system symmetry, whenever possible.

By careful finite-size extrapolation of sufficiently large systems, the TM method can also be used to examine two-dimensional models. A particularly interesting series of such systems are Ising models modified with next-nearest-neighbor frustration, which recapitulate the formation of equilibrium modulated phases in systems as varied as magnetic alloys, lipid surfactants, and cell morphogenesis. In these models, frustration results in large mixing times for Markov chain Monte Carlo simulations, but the TM approach sidesteps this slowdown and thus provides a putatively well-controlled computational scheme. The effectiveness of TM approach for these models, however, had previously been obfuscated by the limited range of system sizes computationally available for the numerical analysis. In this thesis, I build on the sparse matrix decomposition and take advantage of the structure and symmetry of the TM to develop optimized algorithms for the method, and thereby overcome the computational challenge. The resulting algorithm is implemented in various canonical frustrated next-nearest-neighbor Ising models, aiming to solve long-standing physical problems in these models. The approach provides benchmark results for related statistical physics models. It could also inspire the development of adapted eigensolver for similarly structured matrices.

Item Open Access Percolation thresholds on high-dimensional D_{n} and E_{8}-related lattices.(Physical review. E, 2021-06) Hu, Yi; Charbonneau, PatrickThe site and bond percolation problems are conventionally studied on (hyper)cubic lattices, which afford straightforward numerical treatments. The recent implementation of efficient simulation algorithms for high-dimensional systems now also facilitates the study of D_{n} root lattices in n dimensions as well as E_{8}-related lattices. Here, we consider the percolation problem on D_{n} for n=3 to 13 and on E_{8} relatives for n=6 to 9. Precise estimates for both site and bond percolation thresholds obtained from invasion percolation simulations are compared with dimensional series expansion based on lattice animal enumeration for D_{n} lattices. As expected, the bond percolation threshold rapidly approaches the Bethe lattice limit as n increases for these high-connectivity lattices. Corrections, however, exhibit clear yet unexplained trends. Interestingly, the finite-size scaling exponent for invasion percolation is found to be lattice and percolation-type specific.Item Open Access The dimensional evolution of structure and dynamics in hard sphere liquids(2021-11-26) Charbonneau, Patrick; Hu, Yi; Kundu, Joyjit; Morse, Peter KThe formulation of the mean-field, infinite-dimensional solution of hard sphere glasses is a significant milestone for theoretical physics. How relevant this description might be for understanding low-dimensional glass-forming liquids, however, remains unclear. These liquids indeed exhibit a complex interplay between structure and dynamics, and the importance of this interplay might only slowly diminish as dimension $d$ increases. A careful numerical assessment of the matter has long been hindered by the exponential increase of computational costs with $d$. By revisiting a once common simulation technique involving the use of periodic boundary conditions modeled on $D_d$ lattices, we here partly sidestep this difficulty, thus allowing the study of hard sphere liquids up to $d=13$. Parallel efforts by Mangeat and Zamponi [Phys. Rev. E 93, 012609 (2016)] have expanded the mean-field description of glasses to finite $d$ by leveraging standard liquid-state theory, and thus help bridge the gap from the other direction. The relatively smooth evolution of both structure and dynamics across the $d$ gap allows us to relate the two approaches, and to identify some of the missing features that a finite-$d$ theory of glasses might hope to include to achieve near quantitative agreement.Item Open Access The dimensional evolution of structure and dynamics in hard sphere liquids.(The Journal of chemical physics, 2022-04) Charbonneau, Patrick; Hu, Yi; Kundu, Joyjit; Morse, Peter KThe formulation of the mean-field infinite-dimensional solution of hard sphere glasses is a significant milestone for theoretical physics. How relevant this description might be for understanding low-dimensional glass-forming liquids, however, remains unclear. These liquids indeed exhibit a complex interplay between structure and dynamics, and the importance of this interplay might only slowly diminish as dimension d increases. A careful numerical assessment of the matter has long been hindered by the exponential increase in computational costs with d. By revisiting a once common simulation technique involving the use of periodic boundary conditions modeled on D_{d}lattices, we here partly sidestep this difficulty, thus allowing the study of hard sphere liquids up to d = 13. Parallel efforts by Mangeat and Zamponi [Phys. Rev. E 93, 012609 (2016)] have expanded the mean-field description of glasses to finite d by leveraging the standard liquid-state theory and, thus, help bridge the gap from the other direction. The relatively smooth evolution of both the structure and dynamics across the d gap allows us to relate the two approaches and to identify some of the missing features that a finite-d theory of glasses might hope to include to achieve near quantitative agreement.Item Open Access Tissue self-organization underlies morphogenesis of the notochord.(Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2018-09) Norman, James; Sorrell, Emma L; Hu, Yi; Siripurapu, Vaishnavi; Garcia, Jamie; Bagwell, Jennifer; Charbonneau, Patrick; Lubkin, Sharon R; Bagnat, MichelThe notochord is a conserved axial structure that in vertebrates serves as a hydrostatic scaffold for embryonic axis elongation and, later on, for proper spine assembly. It consists of a core of large fluid-filled vacuolated cells surrounded by an epithelial sheath that is encased in extracellular matrix. During morphogenesis, the vacuolated cells inflate their vacuole and arrange in a stereotypical staircase pattern. We investigated the origin of this pattern and found that it can be achieved purely by simple physical principles. We are able to model the arrangement of vacuolated cells within the zebrafish notochord using a physical model composed of silicone tubes and water-absorbing polymer beads. The biological structure and the physical model can be accurately described by the theory developed for the packing of spheres and foams in cylinders. Our experiments with physical models and numerical simulations generated several predictions on key features of notochord organization that we documented and tested experimentally in zebrafish. Altogether, our data reveal that the organization of the vertebrate notochord is governed by the density of the osmotically swelling vacuolated cells and the aspect ratio of the notochord rod. We therefore conclude that self-organization underlies morphogenesis of the vertebrate notochord.This article is part of the Theo Murphy meeting issue on 'Mechanics of development'.