Active Jamming: Self-propelled soft particles at high density

We study numerically the phases and dynamics of a dense collection of self-propelled particles with soft repulsive interactions in two dimensions. The model is motivated by recent in vitro experiments on confluent monolayers of migratory epithelial and endothelial cells. The phase diagram exhibits a liquid phase with giant number fluctuations at low packing fraction and high self-propulsion speed and a jammed phase at high packing fraction and low self-propulsion speed. The dynamics of the jammed phase is controlled by the low frequency modes of the jammed packing.Comment: 4 pages, 4 figure

Structure and mechanics of active colloids

11 pages Acknowledgments MCM thanks Xingbo Yang and Lisa Manning for their contribution to some aspects of the work reviewed here and for fruitful discussions. MCM was supported by NSF-DMR-305184. MCM and AP acknowledge support by the NSF IGERT program through award NSF-DGE-1068780. MCM, AP and DY were additionally supported by the Soft Matter Program at Syracuse University. AP acknowledges use of the Syracuse University HTC Campus Grid which is supported by NSF award ACI-1341006. YF was supported by NSF grant DMR-1149266 and the Brandeis Center for Bioinspired Soft Materials, an NSF MRSEC, DMR-1420382.Peer reviewedPreprin

Active swarms on a sphere

Here we show that coupling to curvature has profound effects on collective motion in active systems, leading to patterns not observed in flat space. Biological examples of such active motion in curved environments are numerous: curvature and tissue folding are crucial during gastrulation, epithelial and endothelial cells move on constantly growing, curved crypts and vili in the gut, and the mammalian corneal epithelium grows in a steady-state vortex pattern. On the physics side, droplets coated with actively driven microtubule bundles show active nematic patterns. We study a model of self-propelled particles with polar alignment on a sphere. Hallmarks of these motion patterns are a polar vortex and a circulating band arising due to the incompatibility between spherical topology and uniform motion - a consequence of the hairy ball theorem. We present analytical results showing that frustration due to curvature leads to stable elastic distortions storing energy in the band.Comment: 5 pages, 4 figures plus Supporting Informatio

Critical jamming of frictional grains in the generalized isostaticity picture

While frictionless spheres at jamming are isostatic, frictional spheres at jamming are not. As a result, frictional spheres near jamming do not necessarily exhibit an excess of soft modes. However, a generalized form of isostaticity can be introduced if fully mobilized contacts at the Coulomb friction threshold are considered as slipping contacts. We show here that, in this framework, the vibrational density of states (DOS) of frictional discs exhibits a plateau when the generalized isostaticity line is approached. The crossover frequency to elastic behavior scales linearly with the distance from this line. Moreover, we show that the frictionless limit, which appears singular when fully mobilized contacts are treated elastically, becomes smooth when fully mobilized contacts are allowed to slip.Comment: 4 pages, 4 figures, submitted to PR

A statistical mechanics framework for static granular matter

The physical properties of granular materials have been extensively studied in recent years. So far, however, there exists no theoretical framework which can explain the observations in a unified manner beyond the phenomenological jamming diagram [1]. This work focuses on the case of static granular matter, where we have constructed a statistical ensemble [2] which mirrors equilibrium statistical mechanics. This ensemble, which is based on the conservation properties of the stress tensor, is distinct from the original Edwards ensemble and applies to packings of deformable grains. We combine it with a field theoretical analysis of the packings, where the field is the Airy stress function derived from the force and torque balance conditions. In this framework, Point J characterized by a diverging stiffness of the pressure fluctuations. Separately, we present a phenomenological mean-field theory of the jamming transition, which incorporates the mean contact number as a variable. We link both approaches in the context of the marginal rigidity picture proposed by [3, 4].Comment: 21 pages, 15 figure

Simulation of elongated bubbles in a channel using the two-fluid model

This paper investigates the capability of the two-fluid model to predict the bubble drift velocity of elongated bubbles in channels. The two-fluid model is widely used in the oil and gas industry for dynamic multiphase pipeline simulations. The bubble drift velocity is an important quantity in predicting pipeline flushing and slug flow. In this paper, it is shown that the two-fluid model in its standard form predicts a bubble drift velocit

Frictional Rigidity Percolation : A New Universality Class and Its Superuniversal Connections through Minimal Rigidity Proliferation

18 pages, 16 figuresPeer reviewedPublisher PD

Investigation of ion-selective nanopores by a multi-level approach

The selective transport of ions through membranes is a known feature of biological and synthetic pores, which remains still not fully understood despite a variety of existing experimental and theoretical investigations with different pore systems.1–3 A deeper understanding of ion selectivity would be desirable for the treatment of related diseases and would have an application in the technical fields of water purification, biosensoric and protein design. For this reason a focus was laid on the theoretical basis of the thermodynamic and kinetic ion selectivity of tetrameric and pentameric ion channels as well as on synthetic channel systems. In a first approach a homology model system for the small viral potassium channel KcvATCV-1 was created and investigated in molecular dynamics simulations with various ion solutions.4 Averaged channel structures, obtained from these simulations, were used to establish and verify a new thermodynamic analysis approach in combination with an integral equation theory. To tackle the kinetic aspects of ion selectivity, theoretical conductances were obtained from molecular dynamics simulations and also calculated from integral equation theory, by making use of previous work of Hummer et al.5 A synthetic hydrophobic pore system of Gong et al.6 was supposed to be appropriate for this investigation, as it fulfilled the assumptions made by Hummer et al.5 The calculated conductances from the independent methods showed a qualitative agreement between them and revealed an anion selectivity of this pore system. The established thermodynamic and kinetic analysis techniques were also used to shed light on the putative pentameric ion channel phospholamban, as it is a biological membrane protein with a hydrophobic character. Compared to experimentally measured conductances by Smeazzetto et al. the calculated conductances could reproduce the observed cation over anion selectivity as well as the inter-cationic selectivity order. In the course of this investigation a hydrophobic restriction was identified to play a significant role for the ion selectivity as identified by the thermodynamic analysis of phospholamban. Formulation of a thermodynamic cycle permitted the investigation of single solvation free energy contributions to the cation over anion selectivity and the inter-cationic selectivity. This investigations identified strong global and local solvation effects to control the observed selectivity. In this work, the influence of the solvent on thermodynamic and kinetic selectivity in polar and hydrophobic ion channels has been revealed.Der selektive Transport von Ionen durch Membranen ist eine bekannte Eigenschaft von biologischen sowie synthetischen Poren, die bis heute trotz einer Vielzahl an existierenden theoretischen und praktischen Studien an verschiedensten Porensystemen nicht vollständig aufgeklärt wurde.1–3 Ein tieferes Verständnis von Ionenselektivität würde die Behandlung von damit verbunden Krankheitsbildern erleichtern und wäre in den technischen Bereichen der Wasseraufbereitung, Biosensorik und im Bereich des Proteindesigns von großem Nutzen. Aus diesen Gründen steht die theoretische Erforschung der thermodynamischen und kinetischen Ionenselektivität von biologischen tetrameren und pentameren sowie synthetischen Kanalsystemen im Fokus dieser Arbeit. Hierzu wurde in einem ersten Ansatz ein Homologiemodell des kleinen viralen tertrameren Ionenkanals KcvATCV-1 erstellt und in Molekulardynamik-Simulationen mit verschiedenen Ionenlösungen untersucht.4 Anhand simulationsbasierter symmetrischer Strukturen dieses biologischen Kanals wurde eine thermodynamische Analysemethodik in Kombination mit einer Integralgleichungstheorie etabliert und verifiziert. Um die kinetischen Aspekte der Ionenselektivität zu untersuchen wurden theoretische Leitfähigkeiten auf Basis von Molekulardynamik-Simulationen sowie Ergebnissen von Integralgleichungsberechnungen unter Verwendung der Vorarbeiten von Hummer et al.5 berechnet. Für diese vergleichenden Arbeiten wurde ein geeignetes hydrophobes synthetisches Porensystem von Gong et al. ausgewählt, welches die Annahmen von Referenz 5 erfüllen.5–7 Das Ergebnis dieser Untersuchung zeigte eine qualitative Übereinstimmung der Leitfähigkeiten zwischen beiden Methoden, welche im Fall dieser Pore eine starke Anionen-Selektivität nachwiesen. Auf Grund seiner hydrophoben und gleichzeitig biologischen Eigenschaften wurde die etablierte Analysemethodik abschließend auf den putativen pentameren Ionenkanal Phospholamban angewandt. Hierbei konnte eine mit experimentellen Ergebnissen von Smeazzetto et al. übereinstimmende Kationen-über-Anionen Selektivität nachgewiesen werden, welche zusätzlich die richtige Inter-Kationen-Leitfähigkeiten reproduzierte. Durch die thermodynamische Analyse wurde eine hydrophobe Engstelle als mögliches Selektivitätselement identifiziert. Durch die Formulierung eines thermodynamischen Kreisprozess wurden der lokale und globale Einfluss von Solvatationsbeiträgen im Hinblick auf Ihren Einfluss auf die Kationen-über-Anionen-Selektivität und Inter-Kationen-Selektivität untersucht. Diese Studien zeigten eine große Abhängigkeit beider Selektivitäten von Solvatationseffekten. Zusammengefasst konnte in dieser Arbeit der Einfluss des Solvens auf die thermodynamische und kinetische Selektivität von polaren und hydrophoben Ionenkanälen gezeigt werden

Dynamical patterns in nematic active matter on a sphere

Using agent-based simulations of self-propelled particles subject to short-range repulsion and nematic alignment we explore the dynamical phases of a dense active material confined to the surface of a sphere. We map the dynamical phase diagram as a function of curvature, alignment strength and activity and reproduce phases seen in recent experiments on active microtubules moving on the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1/2 defects. As the driving is increased, geodesic forces drive the transition to a band of polar matter wrapping around an equator, with large bald spots corresponding to two +1 defects at the poles. Finally, bands fold onto themselves, followed by the system moving into a turbulent state marked by active proliferation of pairs of topological defects. We highlight the role of nematic persistence length and time for pattern formation in these confined systems with finite curvature.Comment: 10 pages, 9 figures, includes S