Soft Condensed Matter
New submissions
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New submissions for Mon, 13 May 24
- [1] arXiv:2405.06044 [pdf, other]
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Title: Active nematic fluids on Riemannian 2-manifoldsSubjects: Soft Condensed Matter (cond-mat.soft); Mathematical Physics (math-ph)
Recent advances in cell biology and experimental techniques using reconstituted cell extracts have generated significant interest in understanding how geometry and topology influence active fluid dynamics. In this work, we present a comprehensive continuous theory and computational method to explore the dynamics of active nematic fluids on arbitrary surfaces without topological constraints. The fluid velocity and nematic order parameter are represented as the sections of the complex line bundle of a 2-manifold. We introduce the Levi-Civita connection and surface curvature form within the framework of complex line bundles. By adopting this geometric approach, we introduce a gauge-invariant discretization method that preserves the continuous local-to-global theorems in differential geometry. We establish a nematic Laplacian on complex functions that can accommodate fractional topological charges through the covariant derivative on the complex nematic representation. We formulate advection of the nematic field based on a unifying definition of the Lie derivative, resulting in a stable geometric semi-Lagrangian discretization scheme for transport by the flow. In general, the proposed surface-based method offers an efficient and stable means to investigate the influence of local curvature and global topology on the 2D hydrodynamics of active nematic systems. Moreover, the complex line representation of the nematic field and the unifying Lie advection present a systematic approach for generalizing our method to active $k$-atic systems.
- [2] arXiv:2405.06082 [pdf, other]
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Title: Thermodynamic Insights into Polyelectrolyte Complexation: A Theoretical FrameworkAuthors: Souradeep GhoshSubjects: Soft Condensed Matter (cond-mat.soft)
In this study, we propose a theoretical framework to investigate the interactions between flexible polymer chains, specifically polyelectrolytes (PEs). By calculating the system's free energy while considering position-dependent mutual interactions and chain conformations, we gain insights into the local dielectricity as PEs overlap. Our analysis reveals that the thermodynamic drive for complex coacervation is influenced by factors such as the number of ions bound to the polymer backbone and the entropy associated with free ions, challenging earlier assumptions about the relationship between entropy gain and electrostatic temperature. We demonstrate that global thermodynamic behavior is strongly influenced by local factors like dielectric constant, providing clarity on discrepancies between experimental and computational studies. Additionally, we found that entropy gain is inversely proportional to the local dielectric constant, assuming a constant electrostatic temperature. Our findings highlight the importance of considering polymer-specific parameters when exploring the thermodynamic behavior of charged polymer complexation.
- [3] arXiv:2405.06494 [pdf, other]
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Title: Experimental identification of topological defects in 2D colloidal glassAuthors: Vinay Vaibhav, Arabinda Bera, Amelia C. Y. Liu, Matteo Baggioli, Peter Keim, Alessio ZacconeSubjects: Soft Condensed Matter (cond-mat.soft); Disordered Systems and Neural Networks (cond-mat.dis-nn); Materials Science (cond-mat.mtrl-sci); Other Condensed Matter (cond-mat.other); Statistical Mechanics (cond-mat.stat-mech)
Topological defects are singularities in the order parameter space that are mathematically described by topological invariants and cannot be removed by continuous transformations. These defects play a significant role in various fields, ranging from cosmology to solid-state physics and biological matter. The definition of these irregularities requires an ordered reference configuration, leading to decades of debate about the existence of topological defects in disordered systems, such as glasses. Recently, it has been proposed that well-defined topological defects might emerge in the dynamical properties of glasses under deformation, potentially relating to their plastic behavior. In this study, we investigate a two-dimensional colloidal glass system composed of particles interacting by an effective magnetic repulsion. We reveal the presence of topological defects in the eigenspace of the vibrational frequencies of this experimental 2D amorphous solid. The vibrational density of states of this 2D amorphous material exhibits distinct glassy properties such as the presence of a boson peak anomaly. Through extensive numerical and theoretical quantitative analysis, we establish a robust positive correlation between the vibrational characteristics and the total number of topological defects. We furthermore show that defects of opposite charge tend to pair together and prove their local statistical correlation with the "soft spots", the regions more prone to plastic flow. This work provides the experimental confirmation for the existence of topological defects in disordered systems revealing a complex interplay between topology, disorder, and vibrational behavior.
- [4] arXiv:2405.06537 [pdf, other]
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Title: A self-consistent current response theory of jamming and vibrational modes in low-temperature amorphous solidsComments: 12 pages, 7 appendices, and 6 figuresSubjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech)
We study amorphous solids with strong elastic disorder and find an un-jamming instability that exists, inter alia, in an harmonic model built using Euclidean random matrices (ERM). Employing the Zwanzig-Mori projection operator formalism and Gaussian factorization approximations, we develop a first-principles, self-consistent theory of transverse momentum correlations in athermal disordered materials, extending beyond the standard Born approximation. The vibrational anomalies in glass at low temperatures are recovered in the stable solid limit, and floppy modes lacking restoring forces are predicted in unstable states below the jamming transition. Near the un-jamming transition, the speed of sound $v_0^\perp$ vanishes with $ \propto \sqrt{\epsilon}$, where $\epsilon$ denotes the distance from the critical point. Additionally, the density of states develops a plateau, independent of $\epsilon$ above a frequency $\omega_*$ which vanishes at the transition, $\omega_*\propto |\epsilon|$. We identify a characteristic length scale in the un-jammed phase, $\lambda_-^\perp\propto1/\sqrt{\epsilon}$, indicating the distance over which injected momentum remains correlated. We confirm the theoretical predictions with numerical solutions of a scalar ERM model, demonstrating overall good qualitative and partly quantitative agreement.
- [5] arXiv:2405.06592 [pdf, other]
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Title: Density and inertia effects on two-dimensional active semiflexible filament suspensionsSubjects: Soft Condensed Matter (cond-mat.soft)
We examine the influence of density on the transition between chain and spiral structures in planar assemblies of active semiflexible filaments, utilizing detailed numerical simulations. We focus on how increased density, and higher P\'eclet numbers, affect the activity-induced transition spiral state in a semiflexible, self-avoiding active chain. Our findings show that increasing the density causes the spiral state to break up, reverting to a motile chain-like shape. This results in a density-dependent reentrant phase transition from spirals back to open chains. We attribute this phenomenon to an inertial effect observed at the single polymer level, where increased persistence length due to inertia has been shown in recent three-dimensional studies to cause polymers to open up. Our two-dimensional simulations further reveal that a reduction in the damping coefficient leads to partial unwinding of the spirals, forming longer arms. In suspension, interactions among these extended arms can trigger a complete unwinding of the spirals, driven by the combined effects of density and inertia.
- [6] arXiv:2405.06614 [pdf, other]
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Title: An explicit granular-mechanics approach to marine sediment acousticsComments: Accepted for publication in the Journal of the Acoustical Society of AmericaSubjects: Soft Condensed Matter (cond-mat.soft); Geophysics (physics.geo-ph)
Here we theoretically and computationally study the frequency dependence of phase speed and attenuation for marine sediments from the perspective of granular mechanics. We leverage recent theoretical insights from the granular physics community as well as discrete-element method simulations, where the granular material is treated as a packing of discrete objects that interact via pairwise forces. These pairwise forces include both repulsive contact forces as well as dissipative terms which may include losses from the fluid as well as losses from inelasticity at grain-grain contacts. We show that the structure of disordered granular packings leads to anomalous scaling laws for frequency-dependent phase speed and attenuation that do not follow from a continuum treatment. Our results demonstrate that granular packing structure, which is not explicitly considered in existing models, may play a crucial role in a complete theory of sediment acoustics. While this simple approach does not explicitly treat sound propagation or inertial effects in the interstitial fluid, it provides a starting point for future models that include these and other more complex features.
- [7] arXiv:2405.06638 [pdf, ps, other]
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Title: Assorted remarks on bending measures and energies for plates and shells, and their invariance propertiesComments: an extended comment on our and others' works, including a correctionSubjects: Soft Condensed Matter (cond-mat.soft)
In this note, we address several issues, including some raised in recent works and commentary, related to bending measures and energies for plates and shells, and certain of their invariance properties. We discuss the distinction between definitions and results in our and others' approaches, correct an error and citation oversights in our work, and provide additional brief observations regarding the relative size of energetic terms and the symmetrization of bending measures. Particular points of emphasis are a reiteration of some of the early history of dilation-invariant measures, the similarities between all such measures, and the non-dilation-invariance of our recently introduced bending measure for shells and curved rods. In the course of this discussion, we provide a simpler presentation of the elementary, but much overlooked, fact that the additional tangential stretch of material near the mid-surface of a thin body is the product of the mid-surface stretch and the change in curvature.
Cross-lists for Mon, 13 May 24
- [8] arXiv:2405.06207 (cross-list from physics.chem-ph) [pdf, other]
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Title: Nuclear Quantum Effects on the Electronic Structure of Water and IceAuthors: Margaret Berrens, Arpan Kundu, Marcos F. Calegari Andrade, Tuan Anh Pham, Giulia Galli, Davide DonadioComments: 16 pages, 4 figuresSubjects: Chemical Physics (physics.chem-ph); Soft Condensed Matter (cond-mat.soft)
The electronic properties and optical response of ice and water are intricately shaped by their molecular structure, including the quantum mechanical nature of hydrogen atoms. In spite of numerous studies appeared over decades, a comprehensive understanding of the effect of the nuclear quantum motion on the electronic structure of water and ice at finite temperatures remains elusive. Here, we utilize molecular simulations that harness the efficiency of machine-learning potentials and many-body perturbation theory to assess the impact of nuclear quantum effects on the electronic structure of water and hexagonal ice. By comparing the results of path-integral and classical simulations, we find that including nuclear quantum effects leads to a larger renormalization of the fundamental gap of ice, compared to that of water, eventually leading to a comparable gap in the two systems, consistent with experimental estimates. Our calculations suggest that the quantum fluctuations responsible for an increased delocalization of protons in ice, relative to water, are a key factor leading to the enhancement of nuclear quantum effects on the electronic structure of ice.
- [9] arXiv:2405.06348 (cross-list from physics.bio-ph) [pdf, other]
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Title: Local topology and perestroikas in protein structure and folding dynamicsComments: 18 pages, 11 figuresSubjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Mathematical Physics (math-ph); Chemical Physics (physics.chem-ph)
Methods of local topology are introduced to the field of protein physics. This is achieved by explaining how the folding and unfolding processes of a globular protein alter the local topology of the protein's C-alpha backbone through conformational bifurcations. The mathematical formulation builds on the concept of Arnol'd's perestroikas, by extending it to piecewise linear chains using the discrete Frenet frame formalism. In the low-temperature folded phase, the backbone geometry generalizes the concept of a Peano curve, with its modular building blocks modeled by soliton solutions of a discretized nonlinear Schroedinger equation. The onset of thermal unfolding begins when perestroikas change the flattening and branch points that determine the centers of solitons. When temperature increases, the perestroikas cascade, which leads to a progressive disintegration of the modular structures. The folding and unfolding processes are quantitatively characterized by a correlation function that describes the evolution of perestroikas under temperature changes. The approach provides a comprehensive framework for understanding the Physics of protein folding and unfolding transitions, contributing to the broader field of protein structure and dynamics.
Replacements for Mon, 13 May 24
- [10] arXiv:2312.15069 (replaced) [pdf, other]
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Title: Dynamical Facilitation Governs the Equilibration Dynamics of GlassesAuthors: Rahul N. Chacko, François P. Landes, Giulio Biroli, Olivier Dauchot, Andrea J. Liu, David R. ReichmanComments: 21 pages, 16 figures. Supplemental Movies too large for arXiv. Will provide download link once available. Available on request until thenSubjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Chemical Physics (physics.chem-ph)
- [11] arXiv:2401.02595 (replaced) [pdf, other]
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Title: Thermal transport of confined water molecules in quasi-one-dimensional nanotubesSubjects: Soft Condensed Matter (cond-mat.soft); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Computational Physics (physics.comp-ph)
- [12] arXiv:2403.09278 (replaced) [pdf, other]
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Title: Nonlinear Kinematics of Recursive Origami Inspired by the SpidronComments: 16 pages, 8 figures. To Appear in Origami8: Proceedings of the 8th International Meeting on Origami in Science, Mathematics and Education (8OSME), Melbourne, August 16-18, 2024Subjects: Soft Condensed Matter (cond-mat.soft); Differential Geometry (math.DG); Metric Geometry (math.MG); Chaotic Dynamics (nlin.CD)
- [13] arXiv:2403.18974 (replaced) [pdf, other]
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Title: Granular gases under resettingAuthors: Anna S. BodrovaSubjects: Soft Condensed Matter (cond-mat.soft)
- [14] arXiv:2404.09330 (replaced) [pdf, ps, other]
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Title: A universal strategy for decoupling stiffness and extensibility of polymer networksComments: 4 figures; 10 extended figures; 1 extended tableSubjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Chemical Physics (physics.chem-ph)
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