arXiv - PHYS - Soft Condensed Matter最新文献_第4页

A Modular and Extensible CHARMM-Compatible Model for All-Atom Simulation of Polypeptoids 模块化、可扩展、与 CHARMM 兼容的多肽全原子模拟模型

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-09 DOI: arxiv-2409.06103

Alex Berlaga, Kaylyn Torkelson, Aniruddha Seal, Jim Pfaendtner, Andrew L. Ferguson

{"title":"A Modular and Extensible CHARMM-Compatible Model for All-Atom Simulation of Polypeptoids","authors":"Alex Berlaga, Kaylyn Torkelson, Aniruddha Seal, Jim Pfaendtner, Andrew L. Ferguson","doi":"arxiv-2409.06103","DOIUrl":"https://doi.org/arxiv-2409.06103","url":null,"abstract":"Peptoids (N-substituted glycines) are a class of sequence-defined synthetic\u0000peptidomimetic polymers with applications including drug delivery, catalysis,\u0000and biomimicry. Classical molecular simulations have been used to predict and\u0000understand the conformational dynamics of single peptoid chains and their\u0000self-assembly into diverse morphologies including sheets, tubes, spheres, and\u0000fibrils. The CGenFF-NTOID model based on the CHARMM General ForceField has\u0000demonstrated success in enabling accurate all-atom molecular modeling of the\u0000structure and thermodynamic behavior of peptoids. Extension of this force field\u0000to new peptoid side chain chemistries has historically required\u0000parameterization of new side chain bonded interactions against ab initio and/or\u0000experimental data. This fitting protocol improves the accuracy of the force\u0000field but is also burdensome and time consuming, and precludes modular\u0000extensibility of the model to arbitrary peptoid sequences. In this work, we\u0000develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID)\u0000as an extension of CGenFF-NTOID employing a modular decomposition of the\u0000peptoid backbone and side chain parameterizations wherein arbitrary side chain\u0000chemistries within the large family of substituted methyl groups (i.e., -CH3,\u0000-CH2R, -CHRR' -CRR'R'') are directly ported from CGenFF without any additional\u0000reparameterization. We validate this approach against ab initio calculations\u0000and experimental data to to develop a MoSiC-CGenFF-NTOID model for all 20\u0000natural amino acid side chains along with 13 commonly-used synthetic side\u0000chains, and present an extensible paradigm to efficiently determine whether a\u0000novel side chain can be directly incorporated into the model or whether\u0000refitting of the CGenFF parameters is warranted. We make the model freely\u0000available to the community along with a tool to perform automated initial\u0000structure generation.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanistic Origins of Yielding in Hybrid Double Network Hydrogels 混合双网水凝胶的屈服机理起源

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-09 DOI: arxiv-2409.05765

Vinay Kopnar, Adam O'Connell, Natasha Shirshova, Anders Aufderhorst-Roberts

{"title":"Mechanistic Origins of Yielding in Hybrid Double Network Hydrogels","authors":"Vinay Kopnar, Adam O'Connell, Natasha Shirshova, Anders Aufderhorst-Roberts","doi":"arxiv-2409.05765","DOIUrl":"https://doi.org/arxiv-2409.05765","url":null,"abstract":"Hybrid double-network hydrogels are a class of material that comprise\u0000transiently and permanently crosslinked polymer networks and exhibit an\u0000enhanced toughness that is believed to be governed by the yielding of the\u0000transient polymer network. The precise role of the two polymer networks in this\u0000yielding transition and their interplay remains an open question that we\u0000address here through constructing a series of hydrogel designs in which the\u0000interaction within and between the two polymer networks are systematically\u0000inhibited or enhanced. We characterise each of the hydrogel designs using large\u0000amplitude oscillatory shear rheology (LAOS). Inspecting yielding through\u0000elastic stress across hydrogel designs, we elucidate that the hybrid\u0000double-network hydrogel exhibits a two-step yielding behaviour that originates\u0000from to the presence of transient crosslinks. Examining the rheological\u0000response within each oscillatory cycle and across the hydrogel designs, we show\u0000that the micro-structural changes in the transient network are crucial in the\u0000second stage of this yielding. We surmise that the first step of yielding is\u0000determined by the intermolecular interactions between the two polymer networks\u0000by systematically altering the strength of the interactions. These interactions\u0000also influence the second step of yielding, which we show is governed by the\u0000transient intermolecular interactions within the polymer networks. Our study\u0000therefore reveals that the interactions between the polymer networks are as\u0000crucial as within the polymer networks and therefore provides insights into how\u0000the yielding mechanisms in soft composite materials can be identified,\u0000adjusted, and controlled.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"172 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Banded phases in topological flocks 拓扑群中的带状相位

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-08 DOI: arxiv-2409.05198

Charles R. Packard, Daniel M. Sussman

{"title":"Banded phases in topological flocks","authors":"Charles R. Packard, Daniel M. Sussman","doi":"arxiv-2409.05198","DOIUrl":"https://doi.org/arxiv-2409.05198","url":null,"abstract":"Flocking phase transitions found in models of polar active matter are\u0000paradigmatic examples of active phase transitions in soft matter. An\u0000interesting specialization of flocking models concerns a ``topological'' vs\u0000``metric'' choice by which agents are considered to be interacting neighbors.\u0000While recent theoretical work suggests that the order-disorder transition in\u0000these polar aligning models is universally first order, numerical studies have\u0000suggested that topological models may instead have a continuous transition.\u0000Some recent simulations have found that some variations of topologically\u0000interacting flocking agents have a discontinuous transition, but unambiguous\u0000observations of phase coexistence using common Voronoi-based alignment remains\u0000elusive. In this work, we use a custom GPU-accelerated simulation package to\u0000perform million-particle-scale simulations of these Voronoi-Vicsek flocking\u0000models. By accessing such large systems on appropriately long time scales, we\u0000are able to show that a regime of stable phase coexistence between the ordered\u0000and disordered phases, confirming the discontinuous nature of this transition\u0000in the thermodynamic limit.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Testing Adam-Gibbs relationship in tapped Granular Packings 测试攻丝粒状填料中的亚当-吉布斯关系

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-08 DOI: arxiv-2409.04983

Xinyu Ai, Houfei Yuan, Shuyang Zhang, Zhikun Zeng, Hanyu Li, Chengjie Xia, Yujie Wang

{"title":"Testing Adam-Gibbs relationship in tapped Granular Packings","authors":"Xinyu Ai, Houfei Yuan, Shuyang Zhang, Zhikun Zeng, Hanyu Li, Chengjie Xia, Yujie Wang","doi":"arxiv-2409.04983","DOIUrl":"https://doi.org/arxiv-2409.04983","url":null,"abstract":"Disordered granular packings share many similarities with supercooled\u0000liquids, particu-larly in the rapid increase of structural relaxation time\u0000within a narrow range of temperature or packing fraction. However, it is\u0000unclear whether the dynamics of granular materials align with those of their\u0000corresponding thermal hard sphere liquids, and the particular influence of\u0000friction of a granular system remains largely unexplored. Here, we\u0000experimentally study the slow relaxation and the steady state of monodisperse\u0000granular sphere packings with X-ray tomography. We first quantify the\u0000thermodynamic parameters under the Edwards' ensemble, (i.e., effective\u0000temperature and configurational entropy), of granular spheres with varying\u0000friction, and measure their characteristic relaxation time during compaction\u0000processes. We then demonstrate a unified picture of the relaxation process in\u0000granular systems in which the Adam-Gibbs (AG) relationship is generally\u0000followed. These results clarify the close relation-ship between granular\u0000materials and the ideal frictionless hard sphere model.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Designing precise dynamical steady states in disordered networks 在无序网络中设计精确的动态稳定状态

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-08 DOI: arxiv-2409.05060

Marc Berneman, Daniel Hexner

{"title":"Designing precise dynamical steady states in disordered networks","authors":"Marc Berneman, Daniel Hexner","doi":"arxiv-2409.05060","DOIUrl":"https://doi.org/arxiv-2409.05060","url":null,"abstract":"Elastic structures can be designed to exhibit precise, complex, and exotic\u0000functions. While recent work has focused on the quasistatic limit governed by\u0000force balance, the mechanics at a finite driving rate are governed by Newton's\u0000equations. The goal of this work is to study the feasibility, constraints, and\u0000implications of creating disordered structures with exotic properties in the\u0000dynamic regime. The dynamical regime offers responses that cannot be realized\u0000in quasistatics, such as responses at an arbitrary phase, frequency-selective\u0000responses, and history-dependent responses. We employ backpropagation through\u0000time and gradient descent to design spatially specific steady states in\u0000disordered spring networks. We find that a broad range of steady states can be\u0000achieved with small alterations to the structure, operating both at small and\u0000large amplitudes. We study the effect of varying the damping, which\u0000interpolates between the underdamped and the overdamped regime, as well as the\u0000amplitude, frequency, and phase. We show that convergence depends on several\u0000competing effects, including chaos, large relaxation times, a gradient bias due\u0000to finite time simulations, and strong attenuation. By studying the eigenmodes\u0000of the linearized system, we show that the systems adapt very specifically to\u0000the task they were trained to perform. Our work demonstrates that within\u0000physical bounds, a broad array of exotic behaviors in the dynamic regime can be\u0000obtained, allowing for a richer range of possible applications.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Solvent isotopic effect on the phase transition of lyotropic chromonic liquid crystals: Heavy water makes mesogens less charged 溶剂同位素对各向同性色子液晶相变的影响：重水使介质带电量减少

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-08 DOI: arxiv-2409.05097

Jiyong Cheon, Joonwoo Jeong

{"title":"Solvent isotopic effect on the phase transition of lyotropic chromonic liquid crystals: Heavy water makes mesogens less charged","authors":"Jiyong Cheon, Joonwoo Jeong","doi":"arxiv-2409.05097","DOIUrl":"https://doi.org/arxiv-2409.05097","url":null,"abstract":"The interplay among solute and solvent molecules in lyotropic mesophases\u0000governs their physicochemical properties, such as phase behaviors and\u0000viscoelasticity. In our model system, a lyotropic chromonic liquid crystal\u0000(LCLC) made by disodium cromoglycate (DSCG), charged plank-like molecules\u0000self-assemble to form elongated aggregates via non-covalent attractions in\u0000water (H$_{2}$O). The aggregates align to exhibit liquid crystalline phases:\u0000nematic and columnar phases. Here, we report the isotopic effect on the phase\u0000behavior of the LCLC when D$_2$O is substituted for H$_2$O. D$_2$O-DSCG\u0000exhibits higher nematic-to-isotropic phase transition temperatures than\u0000H$_2$O-DSCG. X-ray scattering reveals considerably longer inter-aggregate\u0000correlation lengths in D$_2$O-LCLCs. In contrast, the other microstructural\u0000properties, such as inter-aggregate distances and intra-aggregate correlation\u0000lengths, remain almost the same. Our $^{23}$Na FT-NMR measurement reveals that\u0000D$_2$O-DSCG aggregates are less charged with more counter-ions, Na$^+$, bound\u0000to them than H$_2$O-DSCG aggregates. Weaker electrostatic repulsion between\u0000aggregates may stabilize the nematic phase, and this solvent isotopic effect\u0000may generally apply to diverse aqueous lyotropic mesophases with electrostatic\u0000interactions.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Two-dimensional squishy glass: yielding under oscillatory shear 二维软玻璃：振荡剪切下的屈服

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-07 DOI: arxiv-2409.04725

Sayantan Ghosh, Rahul Nayak, Satyavani Vemparala, Pinaki Chaudhuri

引用次数: 0

Light-Activated Motion, Geometry- and Confinement-Induced Optical Effects of 2D Platelets in a Nematic Liquid Crystal 向列液晶中二维小板的光激活运动、几何和致密光学效应

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-07 DOI: arxiv-2409.04912

Antonio Tavera-Vázquez, Danai Montalvan-Sorrosa, Gustavo Perez-Lemus, Otilio E. Rodriguez-Lopez, Jose A. Martinez-Gonzalez, Vinothan N. Manoharan, Juan J. de Pablo

{"title":"Light-Activated Motion, Geometry- and Confinement-Induced Optical Effects of 2D Platelets in a Nematic Liquid Crystal","authors":"Antonio Tavera-Vázquez, Danai Montalvan-Sorrosa, Gustavo Perez-Lemus, Otilio E. Rodriguez-Lopez, Jose A. Martinez-Gonzalez, Vinothan N. Manoharan, Juan J. de Pablo","doi":"arxiv-2409.04912","DOIUrl":"https://doi.org/arxiv-2409.04912","url":null,"abstract":"Motile liquid crystal (LC) colloids show peculiar behavior due to the high\u0000sensitivity to external stimuli driven by the LC elastic and surface effects.\u0000However, few studies focus on harnessing the LC phase transitions to propel\u0000colloidal inclusions by the nematic-isotropic (NI) interface. We engineer a\u0000quasi-2D active system consisting of solid micron-sized light-absorbent\u0000platelets immersed in a thermotropic nematic LC. The platelets self-propel in\u0000the presence of light while self-inducing a localized NI phase transition. The\u0000sample's temperature, light intensity, and confinement determine three\u0000different regimes: a 2D large regime where the platelet-isotropic phase bubble\u0000is static and the NI interface remains stable; a compact motile-2D regime where\u0000the NI interface lies closer to the platelet's contour; and a\u0000motile-3D-confinement regime characterized by the emergence of multipolar\u0000configurations of the LC. We perform continuum-theory simulations that predict\u0000stationary platelet-LC states when confined in 3D. Our study in an\u0000intrinsically far-from-equilibrium landscape is crucial for designing simple\u0000synthetic systems that contribute to our understanding of harnessing liquid\u0000crystals' phase transitions to propel colloidal inclusions and trigger tunable\u0000topological reconfigurations leading to photonic responses.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Freely Suspended Nematic and Smectic Films and Free-Standing Smectic Filaments in the Ferroelectric Nematic Realm 铁电向列领域中的自由悬浮向列和 Smectic 薄膜以及独立 Smectic 细丝

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-06 DOI: arxiv-2409.04019

Keith G. Hedlund, Vikina Martinez, Xi Chen, Cheol S. Park, Joseph E. Maclennan, Matthew A. Glaser, Noel A. Clark

{"title":"Freely Suspended Nematic and Smectic Films and Free-Standing Smectic Filaments in the Ferroelectric Nematic Realm","authors":"Keith G. Hedlund, Vikina Martinez, Xi Chen, Cheol S. Park, Joseph E. Maclennan, Matthew A. Glaser, Noel A. Clark","doi":"arxiv-2409.04019","DOIUrl":"https://doi.org/arxiv-2409.04019","url":null,"abstract":"We show that stable, freely suspended liquid crystal films can be made from\u0000the ferroelectric nematic ($mathrm{N_F}$) phase and from the recently\u0000discovered polar, lamellar $mathrm{SmZ_A}$ and $mathrm{SmA_F}$ phases. The\u0000$mathrm{N_F}$ films display two-dimensional, smectic-like parabolic focal\u0000conic textures comprising director/polarization bend that are a manifestation\u0000of the electrostatic suppression of director splay in the film plane. In the\u0000$mathrm{SmZ_A}$ and $mathrm{SmA_F}$ phases, the smectic layers orient\u0000preferentially normal to the film surfaces, a condition never found in typical\u0000thermotropic or lyotropic lamellar LC phases, with the $mathrm{SmZ_A}$ films\u0000exhibiting focal-conic fan textures mimicking the appearance of typical\u0000smectics in glass cells when the layers are oriented normal to the plates, and\u0000the $mathrm{SmA_F}$ films showing a texture of plaquettes of uniform in-plane\u0000orientation where both bend and splay are suppressed, separated by grain\u0000boundaries. The $mathrm{SmA_F}$ phase can also be drawn into thin filaments,\u0000in which X-ray scattering reveals that the smectic layer planes are normal to\u0000the filament axis. Remarkably, the filaments are mechanically stable even if\u0000they break, forming free-standing, fluid filaments supported only at one end.\u0000The unique architectures of these films and filaments are stabilized by the\u0000electrostatic self-interaction of the liquid crystal polarization field, which\u0000enables the formation of confined, fluid structures that are fundamentally\u0000different from those of their counterparts made using previously known liquid\u0000crystal phases.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Why Static Friction Decreases From Single to Multi-asperity Contacts 为什么静摩擦力会从单个触头减少到多个触头

arXiv - PHYS - Soft Condensed Matter Pub Date : 2024-09-06 DOI: arxiv-2409.04280

Liang Peng, Thibault Roch, Daniel Bonn, Bart Weber

引用次数: 0