Interdisciplinary challenges in non-equilibrium physics: from soft to active, biological and complex matter

EEA1 is a recently discovered new type of molecular motor that consists of an unusually long coiled-coil protein and a small GTPase. Binding and unbinding of the small GTPase triggers dramatic structural transitions within the ~ 200nm long coiled-coil polymer. These transitions lead to changes in polymer flexibility that drive cycles of contractions and expansions. We developed a Langevin model helps us answer some of the key questions regarding motor proteins: what is the entropy production of the polymer engine as a function of the physical parameters of the system; and how does that relate to the efficiency and power of the motor? We also investigate how the chemical coupling of the underlying reaction network can influence the average behavior of the motor.

Collections of living organisms often exhibit self-organised and chaotic motion. Swarming bacteria and cytoskeleton fibres produce chaotic flows driven by their irreversible metabolic processes, described by active nematics hydrodynamics. When confined in a narrow channel, the suspension starts moving and exhibits different flow patterns, including unidirectional, dancing and turbulent flows [1][2]. Our research addresses the dispersion of a solute driven by the chaotic flows of active nematics in a channel, with possible applications in mixing at the microscale [3][4]. At low activities, there is a net flux along the channel and the phenomenon becomes analogous to Taylor-Aris dispersion. We derive an analytical expression for the effective diffusion coefficient as a function of the activity for this regime. Additionally, we analyze the dispersion in the flow regimes at higher activities. [1] Rodrigo C.V. Coelho, Nuno A.M. Araújo, and Margarida M. Telo Da Gama. “Active nematic-isotropic interfaces in channels”. In: Soft Matter 15.34 (2019). issn: 17446848. doi: 10.1039/c9sm00859d. [2] Jérôme Hardoüin et al. “Reconfigurable flows and defect landscape of confined active nematics”. In: Commun Phys 2.1 (Oct. 4, 2019), p. 121. issn: 2399-3650. doi: 10 . 1038 / s42005 - 019 - 0221 - x. [3] Xiao-Lun Wu and Albert Libchaber. “Particle Diffusion in a Quasi-Two- Dimensional Bacterial Bath”. In: Phys. Rev. Lett. 84.13 (Mar. 27, 2000), pp. 3017–3020. issn: 0031-9007, 1079-7114. doi: 10.1103/PhysRevLett. 84.3017. [4] Patrick T. Underhill, Juan P. Hernandez-Ortiz, and Michael D. Graham. “Diffusion and Spatial Correlations in Suspensions of Swimming Particles”. In: Phys. Rev. Lett. 100.24 (June 16, 2008), p. 248101. issn: 0031-9007, 1079-7114.doi:10.1103/PhysRevLett.100.248101.

Correlation Function for heteropolymers Correlation function between helical states in two-component (A/B) random biopolymers has been investigated in frame of Generalized Model of Polypeptide Chain (GMPC). We calculated dependence of correlation function “g” as a function of distance “D” between helical states. Transfer matrix of GMPC appears as [1,2]: \begin{equation} G_i(\Delta \times \Delta)= \begin{pmatrix} e^{\frac{U_i}{T}} &1&0& \cdots &0&0&0\\ 0 &0&1& \cdots &0&0&0\\ \cdots &\cdots &\cdots &\cdots &\cdots &\cdots &\cdots &\\ 0&0&0 &\cdots & 0&1& 0\\ 0&0&0 &\cdots & 0&0& Q_i-1\\ 1&1&1 &\cdots & 1&1& Q_i-1 \end{pmatrix}, \end{equation} Where $U_i$ is helical state energy, $T$ is the temperature of the system, $Q_i$ is the number of conformations depending on the type of repeated unit, and depending on the number in heteropolymer $i$ corresponds either to “A” or “B” types of repeated units. Correlation function was calculated using multiplication method: \begin{equation} g(D)=\frac{1}{NZ}J_{\Delta D}^*\prod _{i=1}^NM_i\;J_{\Delta D}-\theta^2 \end{equation} And super matrices are: \begin{equation} M_i(D)= \begin{pmatrix} G_i &G_i’&0& \cdots &0&0&0\\ 0 &0&G_i& \cdots &0&0&0\\ \cdots &\cdots &\cdots &\cdots &\cdots &\cdots &\cdots &\\ 0&0&0 &\cdots & 0&G_i& 0\\ 0&0&0 &\cdots & 0&0&G_i’\\ 0&0&0 &\cdots & 0&0&G_i \end{pmatrix}, \end{equation} Where $G_i'$ is similar to transfer matrix, with all elements “0” except for $G_{11}=e^{-\frac{U_i}{T}}$. Tha calculation of partition function ‘Z’ and helicity degree “θ” has been performed the same way as in [1,2]. Results for correlation function are obtained for melting temperature, and for temperature boundaries of melting interval. Based on dependences of ln(g(D)) on D and ln(g(D)) on ln(D) , the following analytic relationship for correlation function and distance between helical states is suggested: \begin{equation} \label{core.f} $g(D)=Ae^{-D/\xi }+BD^{-n}$ (1) \end{equation} Here “A”, “B” и “n”, "ξ” are constants, and the first term in right hand side corresponds to homopolymer dependence with correlation length ξ [3,4]. The second term has been used for spin-glass models [5]. The “A”, “B”, “n” и “ξ” constants were estimated through logarithmic graphs and g(D) curve in melting temperature was fitted with constants with close values using the formula (1) and the constant are obtained as: A ≈ 0.24, B ≈ 0.04, ξ ≈ 59, n=0.21. Conclusions: - The exponential dependence of the correlation function predominates Near the melting temperature, which explains the applicability of homopolymer models for DNA. - The small value of the maximum correlation length ξ compared to the values for the corresponding homopolymers is consistent with the broadening of the transition interval for heteropolymers. - The presence of the order component in g(D) dependence for long tails indicates correlations associated with the heterogeneity of the system and needs further research. References 1. A.V. Asatryan, H.H. Mikayelyan, and V. A. Stepanyan. Journal of Contemporary Physics (Armenian Academy of Sciences) 57, no. 3: 308-312 (2022). 2. Sh.A. Tonoyan, A.V. Asatryan, A.K. Andriasyan, Y.Sh. Mamasakhlisov, and V.F. Morozov. Journal of Biomolecular Structure and Dynamics 33, no. sup1 (2015): 126-126. 3. Flory P.J. Statistical Mechanics of Chain Molecules, New York: Interscience. (1969). 4. Y.Sh. Mamasakhlisov, A.V. Badasyan, A.V. Tsarukyan, A.V. Grigoryan, and V.F. Morozov. arXiv preprint cond-mat/0506791 (2005). 5. Fisher Daniel S., and David A. Huse. Physical Review B 38, no. 1 (1988): 386.

O. Bantysh 1,2, J. Ignés-Mullol 1,2, F. Sagués Mestre 1,2 1. Departament de Química Física, Universitat de Barcelona, Barcelona, Spain 2. Institute of Nanoscience and Nanotechnology, Universitat de Barcelona, Barcelona, Spain We assemble a biomimetic active material from microscopic components like cells' filaments and protein motors that consumes energy and generates continuous motion. Such active systems are capable of self-organization at different length and time scales, often exhibiting turbulent flows and the emergence of long-range orientational order, which is a characteristic of active nematics (AN). Previously, it was demonstrated that, by bringing into contact a two-dimensional AN with an anisotropic oil that features smectic liquid-crystalline order, it is possible to transform the originally turbulent flow of the active fluid into well-aligned flows ordered by a magnetic field [1]. Alternatively, the flow of active nematic could be controlled by confining walls [2] or arrangements of obstacles [3]. In present work we combine both approaches: well-aligned flows of AN ordered by a magnetic field were confined between walls of PDMS channels. The resulting quasi-laminar flows of AN are perturbed by closely located channel walls and reorganised in array of vortexes forming an hexagonal lattice. The emergence of vortex lattices is correlated with positional ordering of topological defects and the appearance of density patterns. The observed self-organization of the active flows is activity dependent and reflects the inherent properties of the aligned AN. The described system is an example of pattern formation from instabilities of AN flows and suggests potential applications in the design and control of active materials. References: [1] P. Guillamat, et al., Proc. Natl. Acad. Sci. U. S. A., 113, 20 (2016). [2] J.Hardoüin et al., Soft Matter, 16, (2020). [3] B. Zhang, et al., Phys. Rev. Research, 2, 4 (2020).

The liquid-liquid phase separation of intrinsically disordered proteins plays an integral part for the formation of membraneless organelles in cells, which in turn have key functional and regulatory roles. Many studies on LLPS focus on in vitro experiments and bulk simulations in solution, but real-life systems are highly influenced by crowding within a cell as well as the confinement by the cell membrane. To mimic more closely conditions prevalent in cellular environments, we perform coarse-grained molecular simulations [1] of the low-complexity domains of heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) and Fused in Sarcoma (FUS) in spherical confinement, where we systematically vary the fraction of the crowding agent polyethylene glycol (PEG). We further elucidate how the elasticity of a PEG network influences and even limits size and mobility of the protein condensates.

Cellular Potts models are broadly applied across developmental biology and cancer research. We overcome limitations of the traditional approach, which reinterprets a modified Metropolis sampling as ad hoc dynamics, by introducing an interpretable timescale through Poissonian kinetics and by applying principles of stochastic thermodynamics to separate thermal and athermal sources of noise. Our method accurately describes cell-sorting dynamics in mouse embryo development and identifies the distinct contributions of nonequilibrium processes, e.g. cell growth and active fluctuations.

The broad and beautiful ensemble of molluscan shell morphologies and outer shell topographies has been long studied and yet finding an overarching mechanism describing their development remains elusive. This work describes one such mechanism. By correlating between outer topographies and structural and crystallographic properties of the shells taken from three different species of the marine bivalve family Pectinidae, we demonstrate that the ridge patterns across the shells surface is the results of multimodal wrinkling.

Active mixtures are out-of-equilibrium systems composed of different types of self-propelled particles. Examples range from colonies of microorganisms with varying sizes, shapes, and speeds to groups of different species of birds and larger animals. One possible communication strategy utilized by individuals within these systems is chemically tracing the presence of others, a process known as quorum sensing. This mechanism regulates their motility, thereby influencing their spatial distribution. In passive dense mixture systems, such as protein soups, phase separation can occur in two stages. The initial homogeneous state separates into dense and dilute phases with the same global density composition. Over long timescales, the local composition of these phases further changes to minimize the free energy of the system, a phenomenon known as slow fractionation. We investigate whether and how slow fractionation occurs in dense active mixtures undergoing motility-induced phase separation. Using a quorum-sensing interaction model with excluded volume effects, where particles regulate self-propulsion based on the local densities of the system components, we demonstrate how active mixtures also exhibit this slow transient dynamics of local composition. Specifically, we consider cases where our model cannot be coarse-grained to a passive-like behavior, which arises when non-reciprocal interactions are incorporated. Our results offer insights into the pattern formation of living systems and shed light on spatial ecological behaviors, such as species cooperation or competition foraging strategies.

The collective behaviour of self-propelled particles can produce turbulent flows, termed active turbulence. With numerical simulations, we present an intricate activation mechanism for active turbulence in confined active matter. The mechanism builds on the inclusion of contraction-induced flows and a shearthinning fluid in our description. Our results show that contractions can produce an active turbulent state in an otherwise quiescent system. Furthermore, the mixing of passive tracers in the fluid is greatly enhanced in the active turbulent system. The contractions are modelled both with fluid stress perturbations and boundary deformations, using a phase-field model. Our findings provide an inter esting direction in further active matter research, where both the nature of a dynamic microenvironment and non-Newtonian fluids control the appearance of active flows.

The dynamics of colloidal suspensions can be obtained from microscopy images in a number of ways. Single particle tracking is well understood, but is only possible when particle positions can be found and linked between frames to produce trajectories. Differential dynamic microscopy (DDM) can been used to extract dynamics directly from images, without performing particle detection. Here we present a new method to obtain dynamics from images where particle positions can be detected but not linked between frames. This method is based on dividing the observation window into smaller boxes and looking at the fluctuations of the number of particles within a box. We compare these methods and discuss their suitability to other measurement systems such as x-ray projections and confocal microscopy.

This paper presents a discrete element method (DEM) simulations of drag force experienced by spherical shaped intruder moving along different paths in confined granular media. It is revealed that the drag force depends upon friction of both wall-particle and particle-particle and force profile is affected also by nearby walls. We also confirmed that the arch formation in the granular media is responsible for this peculiar behaviour.

In polymers, the equilibrium state is achieved when the chains have access to the maximum number of conformational states, which allows them to explore a larger conformational space, leading to an increase in the entropy of the system. Preparation of thin polymer films using the spin-coating technique results in polymer chains being locked in a nonequilibrium state with lower entropy due to possible stretching of chains during the process. Allowing enough time for recovery results in the relaxation of the spin-coating-induced molecular recoiling stress. Annealing such a film generates entropy due to its inherent irreversibility. We employed the dewetting technique to determine the molecular recoiling stress relaxation time in poly-(tertbutyl styrene) thin films. Furthermore, we qualitatively differentiated the metastable states achieved by the polymer film using entropy generation in a relaxing polymer film as an effect of thermal entropy and associated it with the conformational entropy of polymer chains utilizing the molecular recoiling stress relaxation time. This enabled us to explain molecular recoiling stress relaxation using a rather simplistic approach involving segmental level molecular rearrangements in polymer chains by attaining transient metastable states through an entropically activated process driving toward equilibrium.

Active matter exhibits different non-equilibrium behaviors when confined either via imposed topological boundaries or external fields. Elucidating the dynamics of constituent self-propelling particles is critical to understanding the emergence of these non-equilibrium behaviors. Here we report on our experimental investigations of a metallic Janus particle in an optical harmonic trap [1]. We observed Rosette-like trajectories of the particle especially at high laser power. This is very different dynamics compared to having passive probes under static or intermittent harmonic traps [2,3]. Moreover, at higher laser power, the particle orientation becomes bimodal depending when the particle moves toward or away from the trap. A Langevin formulation which assumes a spatial dependent particle speed that is proportional to the gradient of the beam profile, captures well the experimental data. 1. Mike A. Bonachita, Khate Cheryl C. Bayer, Michael Jade Y. Jerez, Romie Seth E. Florida and Mark Nolan P. Confesor, Dynamics of self-thermophoretic Janus particle in a harmonic optical trap, to be submitted (2024) 2. Michael Jade Y. Jerez and Mark Nolan P. Confesor, Effective Temperature for an Intermittent Bistable Potential, Journal of Chemical Physics 159 (15), 154903 (2023) 3. Michael Jade Y. Jerez, Mike A. Bonachita and Mark Nolan P. Confesor, Reversibility in nonequilibrium steady states as a measure of distance from equilibrium, Physical Review E 104 (4), 044609 (2021)

Non-equilibrium active processes are mostly discussed assuming a clear separation of timescales between the system and environment that eventually leads to an effective Markovian description. However, such assumptions will break down if the environment is viscoelastic as the relaxation time of the fluid will be comparatively higher than the viscous media. The effects of viscoelasticity in shaping different active processes are relatively less explored. Here, with a minimal experiment using a driven colloid in a viscoelastic bath, we show that viscoelasticity significantly increases the mean injected power to the passive object (∼ 50% compared to a viscous medium), for the same strength of the external driving. Additionally, we observe a notable reduction in negative work fluctuations across a wide range of driving amplitudes. These findings along with an increased rate of entropy production suggest an enhanced irreversibility in driven processes within a viscoelastic bath, which we attribute to the emergence of interactions between the colloid and the viscoelastic medium.

Hyperuniformity emerges generically in the coarsening regime of phase- separating fluids. Numerical studies of active and passive systems have shown that the structure factor S(q) behaves as q^ς for q → 0, with hyperuniformity exponent ς = 4. For passive systems, with thermal fluctuations neglected, this result was explained in 1991 by a qualitative scaling analysis of Tomita, exploiting the presence of isotropy at scales much larger than the coarsening length. We reconsider and extend Tomita’s argument to address cases of active phase separation and of non-constant mobility, again finding ς = 4. We further show that dynamical noise of variance D creates a transient ς = 2 regime in d ≥ 2, with a rescaled crossover wavenumber that goes to zero as a power law in time. Conversely, in d = 1, we demonstrate that with noise the ς = 2 regime survives as t → ∞. We confirm our analytical predictions by numerical simulations of continuum theories for active and passive phase separation in the deterministic case and of Model B for the stochastic case.

We present a mesoscopic thin-film model in gradient dynamics form for binary liquid mixtures on brush-covered substrates incorporating volatility in a narrow gap. Thereby, we expand models established in [1, 4–6] by incorporating two substances present in each of three bulk phases - liquid, brush and gas. We discuss the different contributions to the free energy, thereby employing Flory-Huggins theory of mixing for the condensed phases and assuming ideal gases for the vapor phase. Interface energies are modeled as linear interpolations of known limiting cases. The resulting six-field model is then analyzed with numerical time simulations showing results with a focus on lateral concentration gradients, notably at the contact line. Limitations and possible expansions are discussed and briefly outlined. [1] S. Hartmann, C. Diddens, M. Jalaal, and U. Thiele. Journal of Fluid Mechanics, 960, 2023. doi: 10.1017/jfm.2023.176. [2] S. Hartmann, J. Diekmann, D. Greve, and U. Thiele. 2023. doi: 10.48550/ARXIV.2311.07307. [3] S. Schubotz, Q. A. Besford, S. Nazari, P. Uhlmann, E. Bittrich, J.-U. Sommer, and G. K. Auernhammer. Langmuir, 39, 2023. doi: 10.1021/acs.langmuir.2c03009. [4] L. A. Smook, G. C. R. van Eck, and S. de Beer. Macromolecules, 53, 2020. doi: 10.1021/acs.macromol.0c02228. [5] U. Thiele and S. Hartmann. The European Physical Journal Special Topics, 229, 2020. doi:10.1140/epjst/e2020-900231-2. [6] Özlem Kap, S. Hartmann, H. Hoek, S. de Beer, I. Siretanu, U. Thiele, and F. Mugele. The Journal of Chemical Physics, 158, 2023. doi: 10.1063/5.0146779.

In this study, we explore the behavior of a two-dimensional system consisting of magnetic colloids with rod-shaped geometries in the presence of external rotating magnetic fields. Our investigation reveals the emergence of diverse patterns, each contingent on the degree of synchronization between the magnetic rods and the rotating field. We delve into the structural and dynamic attributes of the steady states, exploring how they evolve in response to variations in the rod aspect ratio, the intensity of the external magnetic field, and its rotation frequency. The synchronization behavior of the rods with the magnetic field manifests in three distinct regimes, each associated with specific observed phases and characteristic configurations. Our research culminates in the development of a comprehensive set of phase diagrams, delineating the interplay of external magnetic field magnitude and rotation frequency that results in the distinct self-organized structures.

The filamentous networks that make up the cytoskeleton contribute to transport and mechanical properties within cells [see e.g., 1], as well as (via coupling through the cell wall or membrane) to the general properties of the tissues in which they are embedded. A thorough understanding of the network dynamics of the cytoskeleton could therefore lead to significant insights pertaining to a variety of related properties and processes. This talk will focus on the network dynamics associated with cytoskeletal cross-linking. An analytical approach towards modelling the Langevin dynamics of a system consisting of filaments or polymer chains and generic cross-linker particles, consisting of two beads joined by a spring, will be presented. In order to dynamically model the attachment of the cross-linkers to the beads of the polymer chains, we turn to a Gaussian networking theory [2] suitably adapted for dynamics. This involves the introduction of fields which implement spatial and temporal constraints on the trajectories of the cross-linkers and beads of the polymers. Depending on the manner in which these fields are introduced, one can manipulate these constraints to model either permanent or entirely reversible cross-links. By introducing a statistical advantage for cross-linkers which are attached at both ends, the formalism allows one to utilise this advantage in a generating function to calculate the average number of attached cross-linkers at any given time. Combining the Gaussian networking fields with field theoretical formalisms that model the dynamics of the cross-linkers and of the chains themselves leads to a collective dynamics description with individual chain dynamics coupled to one another via the dynamics of the bead-spring style cross-linkers. This talk will therefore introduce the audience to a novel field theoretical technique, its mechanism and interpretation and show results that may be achieved using this approach. [1] S. Fürthauer and M. J. Shelley, Annual Review of Condensed Matter Physics 13, 365 (2022). [2] S. F. Edwards, Journal de Physique France 49, 1673 (1988).

Material flow in the acto-myosin cortex of a cell, during cell division, has been found to be chiral in nature. Here we look for possible signature of such chirality during the growth of the intra-cellular membrane partition which physically divides the cell into two compartments. Many groups have recorded this partition formation phenomenon in C. elegans embryo, in real time, using fluorescent microscopy. We carry out PIV analysis on such movies to search for signatures of chirality in the acto-myosin flow field on this partition. Further, we use standard hydrodynamic theory of active gel to predict possible chiral flow structures in the growing partition. While the flows in the growing annular shaped membrane partition is dominantly radial, it can also develop non zero azimuthal velocity components (rotation) due to chirality. We show that the direction of rotation (clock or anti-clockwise) is not solely decided by the sign of the active chiral torque, but also by the relative strengths of rotational viscosity and flow coupling parameter.

Active matter is a class of systems characterized by internal energy consumption, giving self-propelled entities that can be associated with large-scale orientational order. In the past two decades, it surged a large research interest, driven by its relevance for the dynamics of biological systems like cell tissues or cell cytoskeleton. In this study, topological defects of charge +1 in a circular 2D polar system were investigated, motivated by their influence on the curvature of tissues in 3D environments. This system is usually described with a hydrodynamic theory of polar active fluids, where active stresses can drive the system's rotation. Contrary to previous works, a departure from rotational symmetry is allowed. A comparative analysis is conducted with an established hydrodynamic model for active polar fluids with internal energy consumption leading to active stress in the system. Through this comparison, deviations arising from numerical considerations and the absence of rotational symmetry were identified and discussed. Investigating boundary conditions and parameters revealed numerical challenges, necessitating a shift to orientational anchoring for effective confinement. Feasible parameters were identified, enabling successful algorithm implementation using the framework OpenFPM. To control topological defects, a non-homogeneous activity pattern was implemented, revealing intriguing dynamics such as self-propulsion and spiral motion initiation. Control strategies using a Proportional-Integral controller offered partial success in manipulating defect trajectories. In summary, this study advances our understanding of +1 defects and provides insights into non-homogeneous activity patterns, contributing to future advancements in cellular manipulation and medical research.

The genomic material in a cell's nucleus is intricately structured in space and time, and nuclear processes like gene transcription or DNA damage repair rely crucially on this physical organization. Recent efforts have highlighted a discrepancy in our understanding of the static and dynamic aspects of this organization, such that the field currently uses two mutually incompatible models to describe structure and movement of the chromatin fiber, respectively. I will first illustrate a theoretical argument to reconcile these observations by considering the interactions between fibers and then present our current effort to study these interactions in vitro.

We study the diffusive behaviour of interacting active particles (self-propelled) with mass $m$ in an asymmetric channel. The particles are subjected to an external oscillatory force along the length of the channel. In this setup, particles may exhibit rectification. In the absence of interaction, the mean velocity $\langle v \rangle$ of the particles shows a maximum at moderate $m$ values. It means that particles of moderate $m$ have higher velocities than the others. However, by incorporating short-range interaction between the particles, $\langle v \rangle$ exhibits an additional peak at lower $m$ values, indicating that particles of lower and moderate $m$ can be separated simultaneously from the rest. Furthermore, by tuning the interaction strength, the self-propelled velocity, and the parameters of the oscillatory force, one can selectively separate the particles of lower $m$, moderate $m$, or both. Empirical relations for estimating the optimal mass as a function of these parameters are discussed. These findings are beneficial for separating the particles of selective $m$ from the rest of the particles.

Deformable particles, such as epithelial cells or soft colloids, are interesting because of the close link between their dynamics and shape changes. The understanding of and, ultimately, the ability to control the behaviours of such systems present novel challenges in physics and technology. Here, we present a minimal model of the hydrodynamics of deformable particles building on the continuum theory of nematic liquid crystals. We report results describing the behaviour of deformable particles in Poiseulle flow and under active driving.

During early development of the syncytial embryo of Drosophila melanogaster, the first nuclei go through successive division cycles together with important cytoplasmic movement, driving the nuclei cloud to expand along the anterior-posterior axis. Previous experiments linking nuclei-produced PP1 to myosin-II recruitment and flow activity, coupled with optogenetic manipulations, have concluded that actomyosin cortical contractions are responsible for this expansion. Still, the dynamics of the underlying long-range mechanochemical coupling between nuclei and the cortex remains unexplored. In this work, we lay the mathematical foundations of the hydrodynamic flows, chemical couplings, and their interplay in the first seven cycles of the development of Drosophila, finding good correspondence with experiments, and making testable predictions for future research.

From bacterial colonies to bird flocks, living in groups offers advantages for predator evasion, foraging efficiency, and collective decision-making. Groups form and persist based on how individuals interact with each other and with the environment around them. In recent years, active colloids have emerged as a microscopic model system for studying group dynamics. In this work, we have used optics to create complex yet controlled energy landscapes and studied the effect of environmental patchiness on the group formation of active colloids (Janus particles). In summary, we demonstrated a non-monotonic relationship between environmental heterogeneity and group dynamics; specifically, we observed that groups become smaller and more stable when the patchiness of the energy landscape is comparable to the size of the particles. Moreover, I will also present how such optical environments can aid in understanding the phototactic behavior of microalgae (Chlamydomonas reinhardtii).

Authors: T. Ihle (1), J. Mihatsch (1), H.-H. Boltz (1), R. Kürsten (2,1) 1) University of Greifswald, Germany 2) University of Barcelona, Spain We study models of self-propelled particles with alignment interactions by means of an active Boltzmann equation [1]. To this end, we evaluate the collision integral directly based on the microscopic equations of motion. This kinetic theory is founded on the assumption of one-sided molecular chaos, a refinement to the molecular chaos assumption underlying commonly employed mean-field approaches. It involves the calculation of the two-particle correlation function in a self-consistent manner, without free parameters [2]. We have introduced the method for Vicsek-type active particles with anti-alignment but without external noise, which allows for an asymptotically exact analytical solution. One direct application is the extraction of the self-diffusion coefficient and the shear viscosity which cannot be done to mean-field order. This exact solution has then been used to study the behaviour of binary mixtures with reciprocal and non-reciprocal interactions, which show the effect of ``Flocking by Turning away'' in certain parameter ranges [3]. In addition to analytical approaches, the methodology allows for numerical calculation of the collision integral in systems that cannot be treated analytically which we use to evaluate the beyond mean-field corrections to the flocking transition under noise. [1] T. Ihle, R. Kürsten, B. Lindner, arXiv:2303.03354 [2] T. Ihle, R. Kürsten, B. Lindner, arXiv:2303.03357 [3] R. Kürsten, J. Mihatsch, T. Ihle, arXiv:2304.05476

There is a recurring theme in cellular vesicle trafficking: unusually long membrane-bound coiled-coil tethering proteins are often paired with specific small globular GTPases on incoming vesicles. Examples include Golgin-245 and Arl1, GMAP-210 and Arf1, or EEA1 and Rab5, with size differences of more than 50-fold between partners. What is the purpose of this unequal pairing of molecules? At early endosomes, binding of the small GTPase Rab5 induces large conformational changes within the coiled-coil tethering protein EEA1, which switches from an extended to a more flexible collapsed state. Previously, we showed that this entropic collapse of EEA1 generates an effective entropic force that can pull tethered membranes closer together [1]. However, it remained unclear whether EEA1 could spontaneously recover from the collapsed state after interaction with the GTPase. Recently, using fluorescence correlation spectroscopy, we showed that EEA1 can undergo multiple cycles of this flexibility transition in a GTPase-dependent manner without the need for additional factors [2]. Based on these observations, we developed a semi-flexible polymer model (Fig. 1) to describe the mechanochemical cycle that drives this two-component molecular motor and to analyze its efficiency. Currently, this coarse-grained model is the basis for stochastic modeling efforts of the motor system. We hope that our work will shed new light on active GTP-driven molecular systems that take advantage of bistable coiled c0il domains in organizing eukaryotic vesicle transport. References: 1. D Murray & M Jahnel et al., An Endosomal Tether Undergoes an Entropic Collapse to Bring Vesicles Together, Nature (2016). 2. A Singh et al., Two-component molecular motor driven by a GTPase cycle. Nature Physics (2023).

The coexistence of liquid and solid phases allows for localisation of key molecules and compounds. Solid surfaces can act as a catalyst and can adsorb and concentrate organic molecules, increasing their local concentrations and enhancing interaction and the likelihood of chemical reactions. This concentration effect is particularly significant in dilute environments, such as early Earth's oceans, where it would have been challenging for complex organic compounds to form without the aid of solid surfaces. Solid phases provide a protective shield for organic molecules against harsh environmental conditions. This protection is vital for the preservation and stability of early organic matter, enabling the development of more intricate and functional molecules. In this work we developed a theoretical model of liquid solid phase coexistence that provide diverse chemical landscapes. Different phases offer distinct chemical conditions and reactivity. Furthermore, we introduced non-equilibrium conditions of precursor cycles in contrast to wet-dry cycles. These cycles speed up chemical processes and leads to a resonance behaviour in the cycle frequency that maximises the chemical turnover, creating selective environments.

Membrane-less organelles formed through intracellular liquid-liquid phase separation play crucial roles in cellular function and dysfunction, including protein aggregation pathologies. Understanding the rheological characteristics and molecular mobility within these condensed-phase droplets is increasingly recognized as essential to elucidate how crowding influences the conformations and interactions of biological macromolecules within these condensed phases. Utilizing an artificial system where BSA proteins are induced to form droplets by their interactions with synthetic polymeric molecules such as PEG acting as crowding agents, we mimic the highly crowded environment of the cytoplasm. Here, we employ different biophysical techniques, such as Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Recovery After Photobleaching (FRAP), to examine the mechanical and dynamic properties of this model system at the molecular level. Our current findings suggest that BSA is highly segregated inside the droplet phase, which is much more viscous (at least 100 times) or even gel-like compared to the fluid supernatant phase surrounding the condensate droplets.

Epithelial cell sheets form protective barriers in organisms and of key importance is thus their ability to heal wounds. During larger scale wound healing, finger-like structures emerge at the boundary of the cell sheet. Many different models of this fingering instability can be found in the literature, but a conclusive explanation for the physical origin of these finger-like structures remains elusive. Here, we use simulations of the microscopic Active Vertex Model (AVM) of cell sheets to study the finger formation. We find, without leader cells and velocity alignment, a parameter range in which finger formation occurs. Analysis of the interior and the boundary of the cell sheet during the finger formation reveals an instability that is different from the rigidity transition observed in vertex models. We connect the instability to (active) interfacial instability literature and we compare the simulations to experiments on MDCK cell sheets. A better understanding of this type of wound healing may prove useful in developments in clinical tissue engineering.

Accurately predicting the viscosity of water confined within nanotubes is vital for various technological applications. Traditional methods have failed in this regard, necessitating a novel approach. We introduced the Jump-corrected Confined Stokes-Einstein (JCSE) method and now employ the same to estimate viscosity and diffusion in superhydrophobic nanotubes. Our study covers a temperature range of 230-300 K and considers three nanotube diameters. Results show that water inside superhydrophobic nanotubes exhibits significantly lower viscosity and higher diffusion than inside hydrophobic nanotubes. Narrower nanotubes and lower temperatures accentuate these effects. Furthermore, wider superhydrophobic nanotubes display lower viscosity than bulk water, with the difference increasing at lower temperatures. This reduction is attributed to weaker water-water interactions caused by lower water density in the interfacial region. These findings highlight the importance of interfacial water density and its influence on nanotube viscosity, shedding light on nanoscale fluid dynamics and opening avenues for diverse applications.

Cytokinesis is well known to be accomplished by the constriction of a contractile ring. However, many exceptions exist in which a cell is divided with an incomplete ring or contractile band, which generates contractile forces while extending around the cell. This modality of cell division is present in unilaterally cleaving embryos and therefore underlies development in many different species. However, the physical mechanisms of how a contractile band with loose ends can be stabilised and ingress remains elusive. We show that gelation of the bulk cytoplasm through the interphase microtubule network is an essential stabilising mechanism that allows the band to be anchored during growth. When the cell cycle transitions to M-phase, the cytoplasm fluidises, reducing the anchoring of the band to the cytoplasm but also allowing the band to ingress. This balance between stability and growth versus instability and ingression repeats for several cell cycles until the division is complete, resulting in a mechanical ratchet that drives cell division without a complete actin ring.

The spatiotemporal organization of eukaryotic DNA is controlled by an intricate combination of thermally activated (passive) and ATP-consuming (active) processes. For instance, for nucleosomes, the first layer of DNA packaging into chromatin, there is thermally induced nucleosome sliding via spontaneous DNA twist defects and active repositioning of nucleosomes. Based on recent experimental insights into the mechanochemical cycle of chromatin remodelers, molecular machines that actively control nucleosome positions, we introduce a model to study the competition between active and passive mechanisms that mobilize nucleosomes. Chromatin remodelers exploit the intrinsic mobility of nucleosomes based on twist defects in the wrapped DNA. In particular, they inject an over- and undertwist defect pair into the wrapped DNA. The energy cost for this twist defect pair can be calculated using a modified rigid base pair model (Olson et al. 1998), which accounts for the sequence-dependent elasticity and geometry of the base pair steps involved. This leads to two different energy landscapes for the action of the chromatin remodeler, namely sequence-dependent twist-pair injection costs for nucleosome sliding to the left and to the right. By using a master equation for jump processes, these energy landscapes can be transferred into probability density distributions of the nucleosome, which shows the attraction of driven nucleosomes to certain DNA regions. Furthermore, for repetitive DNA sequences, such as telomeres, we find thermal ratchets that propel nucleosomes in a preferred direction.

TBA

The actomyosin cortex is crucial for embryogenesis and development. In the nematode C. elegans, the cortex ensures that the one-celled embryo undergoes polarity establishment to set up the major head-tail body axis. This is achieved by cortical flows at the mesoscale, that arise from myosin gradients in the actomyosin meshwork. Gradients in myosin translate into gradients in active tension and torque in the cortex, which in turn are able to drive flows at the mesoscale. Notably, gradients in active torque can generate asymmetric rotational flows in the cortex, that drives the establishment of left-right body axis during embryogenesis. Recent studies in the lab have found that cortical dynamics depend on the temperature at which embryonic development takes place. This is interesting, as nematodes are cold-blooded organisms, and therefore, can undergo development only within an optimal range of temperatures. To take a step forward to further our understanding, we investigate how actomyosin cortical dynamics in the C. elegans zygote are altered by temperature. Using cortical flow profiles in-vivo, we determine the mesoscale material parameters of the cell cortex as a function of temperature. Rho-GTPase activity in the cortex is upstream of activation of key components like myosin and actin-elongator formin. We further investigate the relation between temperature and rho activation to elucidate a mechanism for cortical response to temperature in nematode embryos.

Epigenetic inheritance during cell division is essential for preserving the cell identity and the stability of the overall chromatin structure. The ‘silent’ part of a chromosome, i.e., the heterochromatin, carries one such crucial epigenetic mark that gets diluted on cell division. Here we built a physical model, based on the formation of a bimolecular condensate or ‘droplet’, that promotes restoration of epigenetic marks. Heterochromatin facilitates formation of the ‘droplet’, via a process formally known as ‘Polymer-Assisted Condensation (PAC), that provides a reaction chamber to carry out different post-translational modifications. We have incorporated the chemical reactions through a particle-based simulation and produced in silico analogue of a cell cycle. The proposed mechanism can stabilize the heterochromatin domains over many cell generations by achieving a faithful epigenetic mark restoration. This mechanism may serve as a general framework for other epigenetic system subject to similar underlying biochemistry.

"Abstract: The internal organization of cells is largely determined by the architecture of the microtubule network. Moreover, microtubules serve as a polar track for the transport of molecular motors. In a previous study, we discussed the transport of two different types of molecular motors walking in the opposite direction along microtubules; one of them accumulates to the plus end, and the other one accumulates to the minus end of the microtubules. As a consequence, the two motors segregate into alternating domains, separated by an interface of aligned and oriented microtubules. In this study, we show that the microtubules act as active surfactants and stabilize domains of the two different motors. We derive continuum equations to study the coarsening of the domains and their steady state properties. We then discuss both the instabilities and the steady patterns created by the microtubules for both symmetric and asymmetric mixtures of molecular motors. [1]. “Force balance of opposing diffusive motors generates polarity-sorted microtubule patterns”, Utzschneider et al. (2024). Keywords: Self-assembly, Interfaces, Multi phases"

Surface properties and fluid dynamics within confined spaces are pivotal factors influencing bacterial adhesion -- a critical step in surface colonization and biofilm formation. This phenomenon gains exceptional significance in the context of implantable devices, where biofilm-related infections present daunting clinical challenges due to their resilience against mechanical stresses and antibiotics. Yet, the interplay between surface topography and fluid shear in microbial attachment remains inadequately understood. Here, we employ surface fabrication techniques coupled with microfluidics to investigate the adhesion of both motile and non-motile \textit{Pseudomonas aeruginosa} bacterial strains on sinusoidal patterns and in the presence of flow, across varying shear rates (ranging from 0.4 to 200 \(s^{-1}\)). Our findings revealed that the presence of a patterned surface topography -- having a length scale comparable to the bacterium size -- significantly impacts the local shear rate field, creating stress concentration points that hinder bacterial spatial arrangement, particularly for non-motile species. In turn, as shear rates increase, we observed a `shear-detachment' effect that contrasts with what has been found in the case of flat surfaces. Moreover, when patterns are aligned perpendicular to the flow direction, detachment increases, especially under moderate shear rates. These results provide valuable insights into the interplay between prescribed surface topography and fluid shear forces, shedding light on strategies to delay and frustrate the early stages of biofilm formation. Such insights hold promising implications for the development of innovative strategies to mitigate biofouling and device-associated infections.

We investigate the influence of substrate softness on biofilm growth amending the thin-film model developed by Trinschek et al for rigid solid substrates [1,2] by the inclusion of a simple description of an elastic substrate [3]. Wettability (described in the mesoscopic model by a wetting energy) is a key factor in the transition between arrested and continuous spreading on rigid substrates [2]. Our focus are changes in the spreading process with changing character of the substrate studied by time simulations of 2d drops/biofilms at fixed surface tension and initial drop volume. We find that with increasing softness from rigid via elastic to liquid-like substrate the spreading velocity of the biofilm decreases at fixed biofilm growth rate and wettability. Further, we discus how these changes depend on wettability and growth rate. In particular, we show that the transition between arrested and continuous spreading is for increasing softness shifted towards larger wettability and larger growth rate. [1] S. Trinschek, K. John, and U. Thiele, AIMS Materials Science 3, 1138 (2016). [2] S. Trinschek, K. John, S. Lecuyer, and U. Thiele, Phys. Rev. Lett. 119, 078003 (2017). [3] C. Henkel, J. H. Snoeijer, and U. Thiele, Soft Matter 17, 10359 (2021).

To affect the viscoelasticity of a hydrogel and potentially shape the material from the inside out, active colloidal particles can swim during the network gelation and exert a mechanical pressure from within. The resulting channels and pores designed by the moving colloids could create patterns for ion transport or drug delivery storage. Active colloidal Janus particles are synthesized from polystyrene colloids semi-coated with only ~2nm of platinum. The colloids are added during the mixing of an agar gel solution in order to be active during the gelation process. By varying the amount of the fuel (hydrogen peroxide) added, the motility can be slightly tuned, thereby also affecting the modulus and viscosity of the network. The swimming particles can disrupt the surrounding environment by displacing bonds from forming or by also densifying regions of polymer, and the consequences are determined through the viscoelastic results. The effect of the activity on the structure of the hydrogel is examined via bulk rheology, microrheology, and confocal microscopy.

We show how non-reciprocal ferromagnetic interactions between neighbouring planar spins in two dimensions, affects the behaviour of topological defects. Non-reciprocity is introduced by weighting the coupling strength of the two-dimensional XY model by an anisotropic kernel. As a consequence, in addition to the topological charge $q$, the actual shape (or phase) of the defects becomes crucial to faithfully describe their dynamics. Non-reciprocal coupling twists the spin field, selecting specific defect shapes, dramatically altering the pair annihilation process. Defect annihilation can either be enhanced or hindered, depending on the shape of the defects concerned and the degree of non-reciprocity in the system.

In nonequilibrium systems, a collective movement of microscopic active particles often displays several common emerging properties, such as swarming, motility-induced phase separation, nonequilibrium disorder-order transitions, anomalous density fluctuation, spatiotemporal patterning, and unusual rheological properties. However, those universal aspects of collective behaviors are hardly captured from microscopic particle-based simulation methods. The macroscopic properties obtained from nonlinear hydrodynamic equations are useful for understanding those aspects. Therefore, we start from the numerical Langevin simulations of the microscopic particle dynamics and present a data-driven strategy for the collection of self-propelled particles to develop the hydrodynamics equations. In our method, microscopic particle data is our input. Hence, the hydrodynamics fields are obtained by coarse-graining from the discrete description of particle dynamics. For partial differential equation (PDE) learning, the spectral representation gives the efficient and accurate computation of spatial and temporal derivatives of density and polarization density fields. Using sparse regression on the fields, we generate hydrodynamic equations. The estimated PDEs from microscopic models are beneficial to understanding the universal features of the system in comparison to standard supervised learning. Hence, the macroscopic features will be shared both by microscopic models and hydrodynamic equations.

Perceptual decision-making frequently requires making rapid, reliable choices upon encountering noisy sensory inputs. To better define the statistical processes underlying perceptual decision-making, here we characterize the choices of human participants visualizing a system of nonequilibrium stationary physical dynamics and compare such choices to the performance of an optimal agent computing Wald’s sequential probability ratio test (SPRT). Participants viewed movies of a particle endowed with drifted Brownian dynamics and had to judge the motion as leftward or rightward. Overall, the results uncovered fundamental performance limits, consistent with recently established thermodynamic trade-offs involving speed, accuracy, and dissipation. Specifically, decision times are sensitive to entropy production rates. Moreover, to achieve a given level of observed accuracy, participants require more time than predicted by SPRT, indicating suboptimal integration of available information. In view of such suboptimality, we develop an alternative account based on non-Markovian evidence integration with a memory time constant. Setting the time constant proportionately to the entropy production in the stimuli significantly improved trial-by-trial predictions of decision metrics with respect to SPRT. This study shows that perceptual psychophysics using stimuli rooted in nonequilibrium physical processes provides a robust platform for understanding how the brain takes decisions on stochastic information inputs.

The human brain continuously makes conscious and unconscious de- cisions to navigate everyday life’s complexity. Lacking a central ner- vous system, complex behavior and remarkable decision-making abil- ities have been reported for non-neuronal organisms like unicellular slime molds. Yet, decision-making is solely described as a response to processed information of the environment and focusing on the out- come rather than the decision-making process. We, here, trap the unicellular slime mold Physarum polycephalum in blue light shapes and follow its decision-making process to find an escape route. We find that decision-making is established by a dynamic adaptation of the flow pattern inside the tubular structure of the organism inducing a pressure buildup for overall mass reallocation.

F-actin is a scaffold protein that provides structural support for the cell and mediates its mechanical behaviors. Actin binding proteins (ABP),such as a-actinin and fascin, link F-actin into a polymer network gel.The increase in crosslinking leads to a general increase in rigidity. As a traditional actin severing protein, cofilin has been shown to oligomerize at low pH and induce F-actin crosslinking through the formation of di-sulfide bonds. Given its known role in softening F-actin in bending, we sought to explore how F-actin crosslinking and F-actin softening contribute to the network-scale mechanical properties of cofilactin. We therefore perform rheology in the linear and nonlinear regimes of F-actin networks crosslinked by cofilin and compare them to well-known F-actin crosslinkers. We find that the moduli of cofilactin gel are independent of the cofilin:actin ratio, persisting over two decades. Further, in the nonlinear regime, as prestress increases, we find that cofilactin gel strain stiffens with an exponent of 1. The origin of the exponent arises from cofilin unbinding from F-actin, causing the crosslinking transition from permanent to dynamic under high shear load.

Developing diffusion barrier layer on material interfaces has potential applications in various fields like packaging materials, pharmaceuticals, chemical filtration, microelectronics, medical devices. Although numerous physical and chemical methods have been proposed to generate the diffusion barrier layer, the complexity of fabrication techniques and high manufacturing costs limit their practical utility. Here, we propose an innovative approach to fabricate the diffusion barrier layer by irradiating poly(dimethylsiloxane) (PDMS) with a mid-infrared (lambda: 10,6µm) CO2 laser. This process directly creates a diffusion barrier layer on the PDMS surface by forming heavily crosslinked network in the polymer matrix. The optimal irradiation conditions were investigated by modulating the defocusing distance, laser power, and number of scanning passes. The barrier thickness can reach up to 70 µm as observed by scanning electron microscope (SEM). The attenuated total reflectance (ATR), electron dispersive X-ray (EDX), and X-ray photoelectron spectroscopy (XPS) analyses collectively confirmed the formation of the SiOx structure on the modified surface, based on the decreased methyl group signal, and the increased oxygen/silicon ratio. The diffusion test with the model drugs (Rhodamine B and Donepezil) demonstrated that the modified surface exhibits effective diffusion barrier properties and that the rate of drug diffusion through the modified barrier layer can be controlled by optimization of the irradiation parameters. This novel approach provides the possibility to develop a controllable diffusion barrier layer in a biocompatible polymer with perspective applications in the fields of pharmaceuticals, packing materials, and medical devices. KEYWORDS: Polydimethylsiloxane – PDMS, mid-infrared radiation, diffusion barrier, silicon oxide layer, drug delivery, crack control, transdermal therapeutic system.

RS-proteins are RNA binding proteins that shape photomorphogenesis in plants by regulating alternative splicing (AS) events. Their light dependent appearance within nuclear speckles connects this AS function to their most probable ability to induce or take part in liquid-liquid phase separation (LLPS). These divergent tasks of specific RNA binding and LLPS is reflected by the dual composition of RS proteins: folded domains, that contain the functionally important RNA binding sites are complemented by intrinsically disordered regions (IDRs) which are common players in LLPS. Here we study the influence of the highly charged IDRs and the post translational phosphorylation of their aminoacids on the LLPS using molecular dynamics simulation using common IDP models [1,2]. [1] Tesei et al. (2022) Open Research Europe, 2(94), 94. [2] Rizuan et al. (2022) J Chem Inf Model 62(18), 4474-4485.

An oil-in-water (O/W) emulsion is a mixture of two immiscible liquids in which small oil droplets are dispersed in a water phase. During storage, emulsion droplets may undergo thermodynamic and breakdown processes, for example, creaming which can lead to phase separation. The addition of emulsifiers can delay these processes. In this study, the effect of varying molecular weights of polyethylene glycol (PEG), a hydrophilic linear polymer, as a co-emulsifier in the continuous phase of an O/W emulsion was investigated. A new approach is established using fluorescence microscopy and an emulsion tracking algorithm to measure the viscosity and diffusibility of individual droplets in the continuous phase. Emulsion tracking provides insights into the local mechanical behavior of the system. Results indicate that higher molecular weight PEG solutions increase the viscosity of the continuous phase, resulting in less diffusibility of the droplets. This novel approach provides a deeper understanding of the physicochemical properties of emulsion. Keywords: emulsion, oil, water, polyethylene glycol, polymer, emulsion tracking, fluorescence microscopy