Cooperatively enhanced reactivity and "stabilitaxis" of dissociating oligomeric proteins.

Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11894-11900

J Agudo-Canalejo, P Illien, R Golestanian

Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein complexes assembled from a few proteins. By studying the generic spatial transport properties of such proteins, we investigate here whether their ability to reversibly associate and dissociate may confer on them a functional advantage with respect to nondissociating proteins. In uniform environments with position-independent association-dissociation, we find that enhanced diffusion in the monomeric state coupled to reassociation into the functional oligomeric form leads to enhanced reactivity with localized targets. In nonuniform environments with position-dependent association-dissociation, caused by, for example, spatial gradients of an inhibiting chemical, we find that dissociating proteins generically tend to accumulate in regions where they are most stable, a process that we term "stabilitaxis."

Goldstone modes in the emergent gauge fields of a frustrated magnet

PHYSICAL REVIEW B 101 (2020) 24413

JT Chalker, SJ Garratt

© 2020 American Physical Society. We consider magnon excitations in the spin-glass phase of geometrically frustrated antiferromagnets with weak exchange disorder, focusing on the nearest-neighbor pyrochlore-lattice Heisenberg model at large spin. The low-energy degrees of freedom in this system are represented by three copies of a U(1) emergent gauge field, related by global spin-rotation symmetry. We show that the Goldstone modes associated with spin-glass order are excitations of these gauge fields, and that the standard theory of Goldstone modes in Heisenberg spin glasses (due to Halperin and Saslow) must be modified in this setting.

Exact Phoretic Interaction of Two Chemically Active Particles.

Physical review letters 124 (2020) 168003-

B Nasouri, R Golestanian

We study the nonequilibrium interaction of two isotropic chemically active particles taking into account the exact near-field chemical interactions as well as hydrodynamic interactions. We identify regions in the parameter space wherein the dynamical system describing the two particles can have a fixed point-a phenomenon that cannot be captured under the far-field approximation. We find that, due to near-field effects, the particles may reach a stable equilibrium at a nonzero gap size or make a complex that can dissociate in the presence of sufficiently strong noise. We explicitly show that the near-field effects originate from a self-generated neighbor-reflected chemical gradient, similar to interactions of a self-propelling phoretic particle and a flat substrate.

Mesoscale modelling of polymer aggregate digestion

Current Research in Food Science Elsevier BV 3 (2020) 122-133

JK Novev, A Doostmohammadi, A Zöttl, JM Yeomans

Yang-Baxter integrable Lindblad equations

SciPost Physics SciPost (2020)

FHL Essler, AA Ziolkowska

We consider Lindblad equations for one dimensional fermionic models and quantum spin chains. By employing a (graded) super-operator formalism we identify a number of Lindblad equations than can be mapped onto non-Hermitian interacting Yang-Baxter integrable models. Employing Bethe Ansatz techniques we show that the late-time dynamics of some of these models is diffusive.

How order melts after quantum quenches

PHYSICAL REVIEW B 101 (2020) 41110

M Collura, FHL Essler

© 2020 American Physical Society. Injecting a sufficiently large energy density into an isolated many-particle system prepared in a state with long-range order will lead to the melting of the order over time. Detailed information about this process can be derived from the quantum mechanical probability distribution of the order parameter. We study this process for the paradigmatic case of the spin-1/2 Heisenberg XXZ chain. We determine the full quantum mechanical distribution function of the staggered subsystem magnetization as a function of time after a quantum quench from the classical Néel state. We establish the existence of an interesting regime at intermediate times that is characterized by a very broad probability distribution. Based on our findings we propose a simple general physical picture of how long-range order melts.

Quantum oscillations probe the Fermi surface topology of the nodal-line semimetal CaAgAs

Physical Review Research American Physical Society 2 (2020) 012055(R)

YH Kwan, P Reiss, Y Han, M Bristow, D Prabhakaran, D Graf, A McCollam, S Ashok Parameswaran, AI Coldea

Nodal semimetals are a unique platform to explore topological signatures of the unusual band structure that can manifest by accumulating a nontrivial phase in quantum oscillations. Here we report a study of the de Haas–van Alphen oscillations of the candidate topological nodal line semimetal CaAgAs using torque measurements in magnetic fields up to 45 T. Our results are compared with calculations for a toroidal Fermi surface originating from the nodal ring. We find evidence of a nontrivial π phase shift only in one of the oscillatory frequencies. We interpret this as a Berry phase arising from the semiclassical electronic Landau orbit which links with the nodal ring when the magnetic field lies in the mirror (ab) plane. Furthermore, additional Berry phase accumulates while rotating the magnetic field for the second orbit in the same orientation which does not link with the nodal ring. These effects are expected in CaAgAs due to the lack of inversion symmetry. Our study experimentally demonstrates that CaAgAs is an ideal platform for exploring the physics of nodal line semimetals and our approach can be extended to other materials in which trivial and nontrivial oscillations are present.

Partial equilibration of the anti-Pfaffian edge due to Majorana Disorder

Physical Review Letters American Physical Society 124 (2020) 126801

S Simon, B Rosenow

We consider electrical and thermal equilibration of the edge modes of the Anti-Pfaffian quantum Hall state at ν = 5/2 due to tunneling of the Majorana edge mode to trapped Majorana zero modes in the bulk. Such tunneling breaks translational invariance and allows scattering between Majorana and other edge modes in such a way that there is a parametric difference between the length scales for equilibration of charge and heat transport between integer and Bose mode on the one hand, and for thermal equilibration of the Majorana edge mode on the other hand. We discuss a parameter regime in which this mechanism could explain the recent observation of quantized heat transport [Banerjee et all, Nature 559, 7713 (2018)].

Classical dimers on penrose tilings

Physical Review X American Physical Society 10 (2020) 011005

F Flicker, SH Simon, Parameswaran

Transport in bilayer graphene near charge neutrality: Which scattering mechanisms are important?

Physical Review Letters American Physical Society 124 (2020) 026601

G Wagner, DX Nguyen, S Simon

Active matter in a viscoelastic environment

Physical Review Fluids American Physical Society 5 (2020) 023102

E Plan, J Yeomans, A Doostmohammadi

Active matter systems such as eukaryotic cells and bacteria continuously transform chemical energy to motion. Hence living systems exert active stresses on the complex environments in which they reside. One recurring aspect of this complexity is the viscoelasticity of the medium surrounding living systems: bacteria secrete their own viscoelastic extracellular matrix, and cells constantly deform, proliferate, and self-propel within viscoelastic networks of collagen. It is therefore imperative to understand how active matter modifies, and gets modified by, viscoelastic fluids. Here, we present a two-phase model of active nematic matter that dynamically interacts with a passive viscoelastic polymeric phase and perform numerical simulations in two dimensions to illustrate its applicability. Motivated by recent experiments we first study the suppression of cell division by a viscoelastic medium surrounding the cell. We further show that the self-propulsion of a model keratocyte cell is modified by the polymer relaxation of the surrounding viscoelastic fluid in a non-uniform manner and find that increasing polymer viscosity effectively suppresses the cell motility. Lastly, we explore the hampering impact of the viscoelastic medium on the generic hydrodynamic instabilities of active nematics by simulating the dynamics of an active stripe within a polymeric fluid. The model presented here can provide a framework for investigating more complex dynamics such as the interaction of multicellular growing systems with viscoelastic environments.

Wavefunctionology: The Special Structure of Certain Fractional Quantum Hall Wavefunctions

in Fractional Quantum Hall Effects: New Developments, World Scientific (2020)


Active nematics with anisotropic friction: the decisive role of the flow aligning parameter.

Soft matter (2020)

K Thijssen, JM Yeomans, A Doostmohammadi, L Metselaar

We use continuum simulations to study the impact of anisotropic hydrodynamic friction on the emergent flows of active nematics. We show that, depending on whether the active particles align with or tumble in their collectively self-induced flows, anisotropic friction can result in markedly different patterns of motion. In a flow-aligning regime and at high anisotropic friction, the otherwise chaotic flows are streamlined into flow lanes with alternating directions, reproducing the experimental laning state that has been obtained by interfacing microtubule-motor protein mixtures with smectic liquid crystals. Within a flow-tumbling regime, however, we find that no such laning state is possible. Instead, the synergistic effects of friction anisotropy and flow tumbling can lead to the emergence of bound pairs of topological defects that align at an angle to the easy flow direction and navigate together throughout the domain. In addition to confirming the mechanism behind the laning states observed in experiments, our findings emphasise the role of the flow aligning parameter in the dynamics of active nematics.

Activity induced nematic order in isotropic liquid crystals

Journal of Statistical Physics Springer Nature (2020)

S Santhosh, M Raeisian Nejad, A Doostmohammadi, J Yeomans, SP Thampi

We use linear stability analysis to show that an isotropic phase of elongated particles with dipolar flow fields can develop nematic order as a result of their activity. We argue that ordering is favoured if the particles are flow-aligning and is strongest if the wavevector of the order perturbation is neither parallel nor perpendicular to the nematic director. Numerical solutions of the hydrodynamic equations of motion of an active nematic confirm the results. The instability is contrasted to the well-known hydrodynamic instability of an ordered active nematic.

The 2020 motile active matter roadmap.

Journal of physics. Condensed matter : an Institute of Physics journal 32 (2020) 193001-

G Gompper, RG Winkler, T Speck, A Solon, C Nardini, F Peruani, H Löwen, R Golestanian, UB Kaupp, L Alvarez, T Kiørboe, E Lauga, WCK Poon, A DeSimone, S Muiños-Landin, A Fischer, NA Söker, F Cichos, R Kapral, P Gaspard, M Ripoll, F Sagues, A Doostmohammadi, JM Yeomans, IS Aranson, C Bechinger, H Stark, CK Hemelrijk, FJ Nedelec, T Sarkar, T Aryaksama, M Lacroix, G Duclos, V Yashunsky, P Silberzan, M Arroyo, S Kale

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of 'active matter' in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines. The 2020 motile active matter roadmap of Journal of Physics: Condensed Matter addresses the current state of the art of the field and provides guidance for both students as well as established scientists in their efforts to advance this fascinating area.

Energetics of Pfaffian–anti-Pfaffian domains

Physical review B: Condensed matter and materials physics American Physical Society 101 (2020) 041302(R)

S Simon, M Ippoliti, MP Zaletel, EH Rezayi

In several recent works it has been proposed that, due to disorder, the experimentally observed ν = 5/2 quantum Hall state could be microscopically composed of domains of Pfaffian order along with domains of anti-Pfaffian order. We numerically examine the energetics required for forming such domains and conclude that for the parameters appropriate for recent experiments, such domains would not occur.

"Not-A", representation symmetry-protected topological, and Potts phases in an S-3-invariant chain

PHYSICAL REVIEW B 101 (2020) ARTN 235108

E O'Brien, E Vernier, P Fendley

SerraNA: a program to determine nucleic acids elasticity from simulation data


V Velasco-Berrelleza, M Burman, J Shepherd, M Leake, R Golestanian, A Noy

Abstract The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA , which is an open software that calculates elastic parameters of double-stranded nucleic acids from dinucleotide length up to the whole molecule using ensembles from numerical simulations. The program reveals that global bendability emerge from local periodic bending angles in phase with the DNA helicoidal shape. We also apply SerraNA to the whole set of 136 tetra-bp combinations and we observe a high degree of sequence-dependence for all elastic parameters with differences over 200%. Tetramers with TA and CA base-pair steps are especially flexible, while tetramers containing AA and AT tend to be the most rigid. Our results thus suggest AT-rich motifs generate extreme mechanical properties depending of the exact sequence ordering, which seems critical for creating strong global bendability on longer sequences when phased properly. SerraNA is a tool to be applied in the next generation of interdisciplinary investigations to further understand what determines the elasticity of DNA. <jats:sec id="s6"> Graphical TOC Entry <jats:fig id="ufig1" position="float" orientation="portrait" fig-type="figure"><jats:graphic xmlns:xlink="" xlink:href="004945v2_ufig1" position="float" orientation="portrait" />

Social Cooperativity of Bacteria during Reversible Surface Attachment in Young Biofilms: a Quantitative Comparison of Pseudomonas aeruginosa PA14 and PAO1.

mBio 11 (2020)

CK Lee, J Vachier, J de Anda, K Zhao, AE Baker, RR Bennett, CR Armbruster, KA Lewis, RL Tarnopol, CJ Lomba, DA Hogan, MR Parsek, GA O'Toole, R Golestanian, GCL Wong

What are bacteria doing during "reversible attachment," the period of transient surface attachment when they initially engage a surface, besides attaching themselves to the surface? Can an attaching cell help any other cell attach? If so, does it help all cells or employ a more selective strategy to help either nearby cells (spatial neighbors) or its progeny (temporal neighbors)? Using community tracking methods at the single-cell resolution, we suggest answers to these questions based on how reversible attachment progresses during surface sensing for Pseudomonas aeruginosa strains PAO1 and PA14. Although PAO1 and PA14 exhibit similar trends of surface cell population increase, they show unanticipated differences when cells are considered at the lineage level and interpreted using the quantitative framework of an exactly solvable stochastic model. Reversible attachment comprises two regimes of behavior, processive and nonprocessive, corresponding to whether cells of the lineage stay on the surface long enough to divide, or not, before detaching. Stark differences between PAO1 and PA14 in the processive regime of reversible attachment suggest the existence of two surface colonization strategies. PAO1 lineages commit quickly to a surface compared to PA14 lineages, with early c-di-GMP-mediated exopolysaccharide (EPS) production that can facilitate the attachment of neighbors. PA14 lineages modulate their motility via cyclic AMP (cAMP) and retain memory of the surface so that their progeny are primed for improved subsequent surface attachment. Based on the findings of previous studies, we propose that the differences between PAO1 and PA14 are potentially rooted in downstream differences between Wsp-based and Pil-Chp-based surface-sensing systems, respectively.IMPORTANCE The initial pivotal phase of bacterial biofilm formation known as reversible attachment, where cells undergo a period of transient surface attachment, is at once universal and poorly understood. What is more, although we know that reversible attachment culminates ultimately in irreversible attachment, it is not clear how reversible attachment progresses phenotypically, as bacterial surface-sensing circuits fundamentally alter cellular behavior. We analyze diverse observed bacterial behavior one family at a time (defined as a full lineage of cells related to one another by division) using a unifying stochastic model and show that our findings lead to insights on the time evolution of reversible attachment and the social cooperative dimension of surface attachment in PAO1 and PA14 strains.

Driven quantum dot coupled to a fractional quantum Hall edge

Physical Review B: Condensed Matter and Materials Physics American Physical Society 100 (2019) 245111

G Wagner, DX Nguyen, DL Kovrizhin, S Simon