# Browsing by Subject "Phase Transition"

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Item Open Access Dimensional study of the caging order parameter at the glass transition.(Proc Natl Acad Sci U S A, 2012-08-28) Charbonneau, Patrick; Ikeda, Atsushi; Parisi, Giorgio; Zamponi, FrancescoThe glass problem is notoriously hard and controversial. Even at the mean-field level, little is agreed upon regarding why a fluid becomes sluggish while exhibiting but unremarkable structural changes. It is clear, however, that the process involves self-caging, which provides an order parameter for the transition. It is also broadly assumed that this cage should have a gaussian shape in the mean-field limit. Here we show that this ansatz does not hold. By performing simulations as a function of spatial dimension d, we find the cage to keep a nontrivial form. Quantitative mean-field descriptions of the glass transition, such as mode-coupling theory, density functional theory, and replica theory, all miss this crucial element. Although the mean-field random first-order transition scenario of the glass transition is qualitatively supported here and non-mean-field corrections are found to remain small on decreasing d, reconsideration of its implementation is needed for it to result in a coherent description of experimental observations.Item Open Access Dimensional study of the dynamical arrest in a random Lorentz gas.(Phys Rev E Stat Nonlin Soft Matter Phys, 2015-04) Jin, Yuliang; Charbonneau, PatrickThe random Lorentz gas (RLG) is a minimal model for transport in heterogeneous media. Upon increasing the obstacle density, it exhibits a growing subdiffusive transport regime and then a dynamical arrest. Here, we study the dimensional dependence of the dynamical arrest, which can be mapped onto the void percolation transition for Poisson-distributed point obstacles. We numerically determine the arrest in dimensions d=2-6. Comparison of the results with standard mode-coupling theory reveals that the dynamical theory prediction grows increasingly worse with d. In an effort to clarify the origin of this discrepancy, we relate the dynamical arrest in the RLG to the dynamic glass transition of the infinite-range Mari-Kurchan-model glass former. Through a mixed static and dynamical analysis, we then extract an improved dimensional scaling form as well as a geometrical upper bound for the arrest. The results suggest that understanding the asymptotic behavior of the random Lorentz gas may be key to surmounting fundamental difficulties with the mode-coupling theory of glasses.Item Open Access Emergence of limit-periodic order in tiling models.(Phys Rev E Stat Nonlin Soft Matter Phys, 2014-07) Marcoux, Catherine; Byington, Travis W; Qian, Zongjin; Charbonneau, Patrick; Socolar, Joshua ESA two-dimensional (2D) lattice model defined on a triangular lattice with nearest- and next-nearest-neighbor interactions based on the Taylor-Socolar monotile is known to have a limit-periodic ground state. The system reaches that state during a slow quench through an infinite sequence of phase transitions. We study the model as a function of the strength of the next-nearest-neighbor interactions and introduce closely related 3D models with only nearest-neighbor interactions that exhibit limit-periodic phases. For models with no next-nearest-neighbor interactions of the Taylor-Socolar type, there is a large degenerate class of ground states, including crystalline patterns and limit-periodic ones, but a slow quench still yields the limit-periodic state. For the Taylor-Socolar lattic model, we present calculations of the diffraction pattern for a particular decoration of the tile that permits exact expressions for the amplitudes and identify domain walls that slow the relaxation times in the ordered phases. For one of the 3D models, we show that the phase transitions are first order, with equilibrium structures that can be more complex than in the 2D case, and we include a proof of aperiodicity for a geometrically simple tile with only nearest-neighbor matching rules.Item Restricted Hard-sphere crystallization gets rarer with increasing dimension.(Phys Rev E Stat Nonlin Soft Matter Phys, 2009-12) van Meel, JA; Charbonneau, B; Fortini, A; Charbonneau, PWe recently found that crystallization of monodisperse hard spheres from the bulk fluid faces a much higher free-energy barrier in four than in three dimensions at equivalent supersaturation, due to the increased geometrical frustration between the simplex-based fluid order and the crystal [J. A. van Meel, D. Frenkel, and P. Charbonneau, Phys. Rev. E 79, 030201(R) (2009)]. Here, we analyze the microscopic contributions to the fluid-crystal interfacial free energy to understand how the barrier to crystallization changes with dimension. We find the barrier to grow with dimension and we identify the role of polydispersity in preventing crystal formation. The increased fluid stability allows us to study the jamming behavior in four, five, and six dimensions and to compare our observations with two recent theories [C. Song, P. Wang, and H. A. Makse, Nature (London) 453, 629 (2008); G. Parisi and F. Zamponi, Rev. Mod. Phys. (to be published)].Item Open Access Numerical detection of the Gardner transition in a mean-field glass former.(Phys Rev E Stat Nonlin Soft Matter Phys, 2015-07) Charbonneau, Patrick; Jin, Yuliang; Parisi, Giorgio; Rainone, Corrado; Seoane, Beatriz; Zamponi, FrancescoRecent theoretical advances predict the existence, deep into the glass phase, of a novel phase transition, the so-called Gardner transition. This transition is associated with the emergence of a complex free energy landscape composed of many marginally stable sub-basins within a glass metabasin. In this study, we explore several methods to detect numerically the Gardner transition in a simple structural glass former, the infinite-range Mari-Kurchan model. The transition point is robustly located from three independent approaches: (i) the divergence of the characteristic relaxation time, (ii) the divergence of the caging susceptibility, and (iii) the abnormal tail in the probability distribution function of cage order parameters. We show that the numerical results are fully consistent with the theoretical expectation. The methods we propose may also be generalized to more realistic numerical models as well as to experimental systems.Item Open Access Quantitative model of the phase behavior of recombinant pH-responsive elastin-like polypeptides.(Biomacromolecules, 2010-11-08) Mackay, J Andrew; Callahan, Daniel J; Fitzgerald, Kelly N; Chilkoti, AshutoshQuantitative models are required to engineer biomaterials with environmentally responsive properties. With this goal in mind, we developed a model that describes the pH-dependent phase behavior of a class of stimulus responsive elastin-like polypeptides (ELPs) that undergo reversible phase separation in response to their solution environment. Under isothermal conditions, charged ELPs can undergo phase separation when their charge is neutralized. Optimization of this behavior has been challenging because the pH at which they phase separate, pHt, depends on their composition, molecular weight, concentration, and temperature. To address this problem, we developed a quantitative model to describe the phase behavior of charged ELPs that uses the Henderson-Hasselbalch relationship to describe the effect of side-chain ionization on the phase-transition temperature of an ELP. The model was validated with pH-responsive ELPs that contained either acidic (Glu) or basic (His) residues. The phase separation of both ELPs fit this model across a range of pH. These results have important implications for applications of pH-responsive ELPs because they provide a quantitative model for the rational design of pH-responsive polypeptides whose transition can be triggered at a specified pH.Item Open Access Recursive directional ligation by plasmid reconstruction allows rapid and seamless cloning of oligomeric genes.(Biomacromolecules, 2010-04-12) McDaniel, Jonathan R; Mackay, J Andrew; Quiroz, Felipe García; Chilkoti, AshutoshThis paper reports a new strategy, recursive directional ligation by plasmid reconstruction (PRe-RDL), to rapidly clone highly repetitive polypeptides of any sequence and specified length over a large range of molecular weights. In a single cycle of PRe-RDL, two halves of a parent plasmid, each containing a copy of an oligomer, are ligated together, thereby dimerizing the oligomer and reconstituting a functional plasmid. This process is carried out recursively to assemble an oligomeric gene with the desired number of repeats. PRe-RDL has several unique features that stem from the use of type IIs restriction endonucleases: first, PRe-RDL is a seamless cloning method that leaves no extraneous nucleotides at the ligation junction. Because it uses type IIs endonucleases to ligate the two halves of the plasmid, PRe-RDL also addresses the major limitation of RDL in that it abolishes any restriction on the gene sequence that can be oligomerized. The reconstitution of a functional plasmid only upon successful ligation in PRe-RDL also addresses two other limitations of RDL: the significant background from self-ligation of the vector observed in RDL, and the decreased efficiency of ligation due to nonproductive circularization of the insert. PRe-RDL can also be used to assemble genes that encode different sequences in a predetermined order to encode block copolymers or append leader and trailer peptide sequences to the oligomerized gene.Item Open Access Transition dynamics and magic-number-like behavior of frictional granular clusters.(Phys Rev E Stat Nonlin Soft Matter Phys, 2012-07) Tordesillas, Antoinette; Walker, David M; Froyland, Gary; Zhang, Jie; Behringer, Robert PForce chains, the primary load-bearing structures in dense granular materials, rearrange in response to applied stresses and strains. These self-organized grain columns rely on contacts from weakly stressed grains for lateral support to maintain and find new stable states. However, the dynamics associated with the regulation of the topology of contacts and strong versus weak forces through such contacts remains unclear. This study of local self-organization of frictional particles in a deforming dense granular material exploits a transition matrix to quantify preferred conformations and the most likely conformational transitions. It reveals that favored cluster conformations reside in distinct stability states, reminiscent of "magic numbers" for molecular clusters. To support axial loads, force chains typically reside in more stable states of the stability landscape, preferring stabilizing trusslike, three-cycle contact triangular topologies with neighboring grains. The most likely conformational transitions during force chain failure by buckling correspond to rearrangements among, or loss of, contacts which break the three-cycle topology.