arXiv subjects

Jens-Uwe Sommer

Publications and source records attributed to Jens-Uwe Sommer.

At least 19 recordsLinked to original sources

arXiv2026

Riding the Wave: Polymers in Time-dependent Nonequilibrium Baths

Directed transport is a characteristic feature of numerous biological systems in response to signals such as nutrient and chemical gradients. These signals often depend on time owing to the high complexity of interactions in these systems. In this study, we focus on the steady-state behavior of polymeric systems responding to such time-dependent signals. We model them as ideal Rouse polymers submerged in a nonequilibrium bath, which is described by a spatially and temporally varying self-propulsion wave field. Through a coarse-graining analysis, we show that these polymers display rich emergent response to the temporal stimuli as a function of their length and topology. In particular, long polymers and structures with ring and star topologies ride the wave, displaying a positive drift in the direction of the wave. Whereas, shorter polymers and fully connected structures drift against the wave signal. We confirm these analytical predictions with robust numerical simulations, showing that the response of polymeric systems to temporal stimuli can be controlled by the topology or the length of the polymer.

cond-mat.soft↗

arXiv2026

Self-organization and cyclic positioning of active condensates

Cohesive active assemblies are often regulated by spatially heterogeneous nonequilibrium driving, such as gradients in motility, biochemical turnover, or mechanical activity. Such heterogeneous driving can influence where condensates or cell collectives accumulate, how stable they are, and how they exchange material with their surroundings. However, the minimal physical mechanisms by which activity gradients control the positioning and turnover of cohesive active matter remain unclear. Here, we address this question using a model of attractive active Brownian particles (ABPs) in a spatially varying activity field. Using Brownian dynamics simulations, we show that these particles undergo liquid-gas phase separation, and spatially varying activity fields induce striking emergent dynamics. Attractive active droplets migrate up activity gradients, and at sufficiently high activity, they can fragment or evaporate into a dilute phase. For finite clusters, evaporated ABPs can redistribute through the simulation box, reassemble into new clusters in lower-activity regions, and migrate again toward higher activity, giving rise to cyclic positioning through repeated nucleation, migration, evaporation, and reassembly.

cond-mat.soft↗

arXiv2026

Mechanistic insights into the spatial organization of RNA polymerase proteins and the chromosome in E. coli cells

Along the bacterial chromosome, regions called rrn operons contain genes that are transcribed into ribosomal RNA. These operons are among the most transcriptionally active sites in the genome. It has been observed in E. coli that RNA polymerase (RNAP), while binding to these genetic loci along the chromosome during transcription, forms dense clusters, leading to spatial colocalization of the operons within the cell. Recent experimental evidence suggests that liquid-liquid phase separation contributes to the formation of RNAP clusters, with the antitermination factor NusA playing a key role. We present a simulation model to investigate the mechanisms underlying the formation of these biomolecular condensates. We propose that mutual attraction between NusA proteins, which exhibit a miscibility gap at higher concentrations, drives condensate formation via a polymer-assisted condensation pathway, and we demonstrate how these condensates promote the colocalization of rrn operons. Our results reconcile seemingly disparate experimental observations of chromosomal organization reported in fluorescence-based imaging and Hi-C experiments.

cond-mat.soft↗

arXiv2026

The Influence of Crosslinking and Deformation on Polymer Crystallization and Melting: A Molecular Dynamics Study

We investigate the crystallization of crosslinked and entangled polymers under external deformation using a coarse-grained poly(vinyl alcohol) (CG-PVA) model and molecular dynamics simulations. Following uniaxial deformation, the systems are cooled at a constant rate to form semi-crystalline states and subsequently heated at a constant rate to induce melting. For unstretched systems, network junctions do not significantly affect the nucleation temperature but increase the amorphous fraction and reduce the melting temperature. Uniaxial deformation accelerates nucleation and markedly increases the crystallization temperature, with more strongly crosslinked polymers exhibiting larger shifts that correlate with an enhanced orientation order parameter. We further compare cooling and heating cycles under constant-strain and constant-stress conditions. Under constant stress, crystallization induces additional elongation beyond the initial pre-stretch and leads to pronounced mechanical hysteresis upon heating, a behavior characteristic of reversible shape-memory materials.

cond-mat.soft↗

arXiv2025

Positive Feedback Drives Sharp Swelling of Polymer Brushes near Saturation

We resolve the Schröder paradox for PNiPAAm brushes, showing experimentally that swelling at 100\% relative humidity (RH) matches the liquid state. This occurs via a sharp increase in swelling above 98\%~RH, a behavior standard models fail to explain. Our extended mean-field theory explains this via a positive feedback between swelling and solvent quality, driven by a concentration-dependent $χ$ parameter. The swelling isotherm quantitatively predicts the dynamic wetting crossover: the advancing contact angle at high velocities drops sharply as ambient humidity surpasses the 98\%~RH threshold.

cond-mat.soft↗

arXiv2025

Collective Dynamics in Active Polar Polymer Assemblies

Tangentially driven active polymers (TDAPs), model systems for motor-driven filaments, have been extensively studied in uniform activity fields. Here, we show that an activity gradient breaks fore-aft symmetry, generating net body forces that steer dimers, asters, and larger assemblies toward high-activity regions. Including temporal stochasticity softens the chains, allowing them to bend and wind around other filaments. Once several contacts are established, steric interlocking arrests relative motion and stabilizes the assembly into a hierarchically entangled cluster. These clusters persist for times far exceeding single-chain relaxation and do not appear under deterministic, temporally constant activity. Remarkably, such activity-induced gelation occurs even at polymer concentrations substantially lower than those typically required for passive chains. Our results reveal a new mechanism for activity-induced aggregation, providing new strategies for designing autonomous and reconfigurable microfluidic systems.

cond-mat.soft↗

arXiv2025

Active Transport of Cargo-Carrying and Interconnected Chiral Particles

Directed motion up a concentration gradient is crucial for the survival and maintenance of numerous biological systems, such as sperms moving towards an egg during fertilization or ciliates moving towards a food source. In these systems, chirality - manifested as a rotational torque - plays a vital role in facilitating directed motion. While systematic studies of active molecules in activity gradients exist, the effect of chirality remains little studied. In this study, we examine the simplest case of a chiral active particle connected to a passive particle in a spatially varying activity field. We demonstrate that this minimal setup can exhibit rich emergent tactic behaviors, with the chiral torque serving as the tuning parameter. Notably, when the chiral torque is sufficiently large, even a small passive particle enables the system to display the desired accumulation behavior. Our results further show that in the dilute limit, this desired accumulation behavior persists despite the presence of excluded volume effects. Additionally, interconnected chiral active particles exhibit emergent chemotaxis beyond a critical chain length, with trimers and longer chains exhibiting strong accumulation at sufficiently high chiral torques. This study provides valuable insights into the design principles of hybrid bio-molecular devices of the future.

cond-mat.stat-mech↗

arXiv2024

A self-organised liquid reaction container for cellular memory

Epigenetic inheritance during cell division is essential for preserving cell identity by stabilizing the overall chromatin organisation. Heterochromatin,the condensed and transcriptionally silent fraction of chromatin,is marked by specific epigenetic modifications that are diluted during each cell division. Here we build a physical model,based on the formation of a biomolecular condensate,a liquid 'droplet',that promotes the restoration of epigenetic marks. Heterochromatin facilitates the droplet formation via polymer-assisted condensation(PAC). The resulting condensate serves as a reaction chamber to reconstruct the lost epigenetic marks. We incorporate the enzymatic reactions into a particle-based simulation and monitor the progress of the epigenetic markers through an in silico analogue of the cell cycle. We demonstrate that the proposed mechanism is robust and stabilizes the heterochromatin domains over many cell generations. This mechanism and variations thereof might be at work for other epigenetic marks as well.

physics.bio-ph↗

arXiv2024

Transport of molecules via polymerization in chemical gradients

The transport of molecules for chemical reactions is critically important in various cellular biological processes. Despite thermal diffusion being prevalent in many biochemical processes, it is unreliable for any sort of directed transport or preferential accumulation of molecules. In this paper we propose a strategy for directed motion in which the molecules are transported by active carriers via polymerization. This transport is facilitated by chemical/activity gradients which generate an effective drift of the polymers. By marginalizing out the active degrees of freedom of the system, we obtain an effective Fokker-Planck equation for the Rouse modes of such active-passive hybrid polymers. In particular, we solve for the steady state distribution of the center of mass and its mean first passage time to reach an intended destination. We focus on how the arrangement of active units within the polymer affect its steady-state and dynamic behaviour and how they can be optimized to achieve high accumulation or rapid motility.

cond-mat.soft↗

arXiv2024

Migration and separation of polymers in non-uniform active baths

Polymer-like structures are ubiquitous in nature and synthetic materials. Their configurational and migration properties are often affected by crowded environments leading to non-thermal fluctuations. Here, we study an ideal Rouse chain in contact with a non-homogeneous active bath, characterized by the presence of active self-propelled agents which exert time-correlated forces on the chain. By means of a coarse-graining procedure, we derive an effective evolution for the center of mass of the chain and show its tendency to migrate towards and preferentially localize in regions of high/low bath activity depending on the model parameters. In particular, we demonstrate that an active bath with non-uniform activity can be used to separate efficiently polymeric species with different lengths and/or connectivity.

cond-mat.soft↗

arXiv2023

Nucleation patterns of polymer crystals analyzed by machine learning models

We use machine learning algorithms to detect the crystalline phase in undercooled melts in molecular dynamics simulations. Our classification method is based on local conformation and environmental fingerprints of individual monomers. In particular, we employ self-supervised auto-encoders to compress the fingerprint information and a Gaussian mixture model to distinguish ordered states from disordered ones. The resulting identification of crystalline monomers agrees to a large extent with human-defined classifiers such as the stem-length-based classification scheme as developed in our previous work [C. Luo and J.-U. Sommer, Macromolecules 44 (2011), 1523], but does not require any foreknowledge about the structure of semi-crystalline polymers. Because of its local sensitivity, the method allows the resolution of detailed time patterns of crystalline order before an apparent signature of the transition is visible in thermodynamic properties such as for the specific volume. At a pre-transition point, we observe the highest crystallization efficiency using the fraction of monomers being conserved in the crystalline phase as compared to the number of monomers joining that phase.

cond-mat.soft↗

arXiv2023

Oscillatory force autocorrelations in equilibrium odd-diffusive systems

The force autocorrelation function (FACF), a concept of fundamental interest in statistical mechanics, encodes the effect of interactions on the dynamics of a tagged particle. In equilibrium, the FACF is believed to decay monotonically in time which is a signature of slowing down of the dynamics of the tagged particle due to interactions. Here we analytically show that in odd-diffusive systems, which are characterized by a diffusion tensor with antisymmetric elements, the FACF can become negative and even exhibit temporal oscillations. We also demonstrate that, despite the isotropy, the knowledge of FACF alone is not sufficient to describe the dynamics: the full autocorrelation tensor is required and contains an antisymmetric part. These unusual properties translate into enhanced dynamics of the tagged particle quantified via the self-diffusion coefficient that, remarkably, increases due to particle interactions.

cond-mat.stat-mech↗

arXiv2023

Tailoring the escape rate of a Brownian particle by combining a vortex flow with a magnetic field

The probability per unit time for a thermally activated Brownian particle to escape over a potential well is in general well-described by Kramers theory. Kramers showed that the escape time decreases exponentially with increasing barrier height. The dynamics slow down when the particle is charged and subjected to a Lorentz force due to an external magnetic field. This is evident via a rescaling of the diffusion coefficient entering as a prefactor in the Kramers escape rate without any impact on the barrier-height-dependent exponent. Here we show that the barrier height can be effectively changed when the charged particle is subjected to an external vortex flow. While the external vortex alone does not affect the mean escape time of the particle, when combined with a magnetic field it effectively pushes the fluctuating particle either radially outside or inside depending on its sign relative to that of the magnetic field. In particular, the effective potential over which the particle escapes can be changed to a flat, a stable, and an unstable potential by tuning the signs and magnitudes of the external vortex and the applied magnetic field. Notably, the last case corresponds to enhanced escape dynamics.

cond-mat.stat-mech↗

arXiv2022

Active Colloidal Molecules in Activity Gradients

We consider a rigid assembly of two active Brownian particles, forming an active colloidal dimer, in a gradient of activity. We show analytically that depending on the relative orientation of the two particles the active dimer accumulates in regions of either high or low activity, corresponding to, respectively, chemotaxis and antichemotaxis. Certain active dimers show both chemotactic and antichemotactic behavior, depending on the strength of the activity. Our coarse-grained Fokker-Planck approach yields an effective potential, which we use to construct a nonequilibrium phase diagram that classifies the dimers according to their tactic behavior. Moreover, we show that for certain dimers a higher persistence of the motion is achieved similar to the effect of a steering wheel in macroscopic devices. This work could be useful for designing autonomous active colloidal structures which adjust their motion depending on the local activity gradients.

cond-mat.soft↗

arXiv2022

Active chiral molecules in activity gradients

While the behavior of active colloidal molecules is well studied by now for a constant activity, the effect of activity gradients is much less understood. Here we explore one of the simplest molecules in activity gradients, namely active chiral dimers composed of two particles with opposite active torques of the same magnitude. We show analytically that with increasing torque, the dimer switches its behavior from antichemotactic to chemotactic. The origin of the emergent chemotaxis is the cooperative exploration of activity gradient by the two particles. While one of the particles moves into higher activity regions, the other moves towards lower activity region resulting in a net bias in the direction of higher activity. We do a comparative study of chiral active particles with charged Brownian particles under magnetic field and show that despite the fundamental similarity in terms of their odd-diffusive behavior, their dynamics and chemotactic behavior are generally not equivalent. We demonstrate this explicitly in a dimer composed of oppositely charged active particles, which remains antichemotactic for any magnetic field.

cond-mat.soft↗

arXiv2022

Collisions enhance self-diffusion in odd-diffusive systems

It is generally believed that collisions of particles reduce the self-diffusion coefficient. Here we show that in odd-diffusive systems, which are characterized by diffusion tensors with antisymmetric elements, collisions surprisingly can enhance the self-diffusion. In these systems, due to an inherent curving effect, the motion of particles is facilitated, instead of hindered by collisions leading to a mutual rolling effect. Using a geometric model, we analytically predict the enhancement of the self-diffusion coefficient with increasing density. This counterintuitive behaviour is demonstrated in the archetypal odd-diffusive system of Brownian particles under Lorentz force. We validate our findings by many body Brownian dynamics simulations in dilute systems.

cond-mat.stat-mech↗

arXiv2022

Escape Dynamics in an Anisotropically Driven Brownian Magneto-System

Thermally activated escape of a Brownian particle over a potential barrier is well understood within Kramers theory. When subjected to an external magnetic field, the Lorentz force slows down the escape dynamics via a rescaling of the diffusion coefficient without affecting the exponential dependence on the barrier height. Here, we study the escape dynamics of a charged Brownian particle from a two-dimensional truncated harmonic potential under the influence of Lorentz force due to an external magnetic field. The particle is driven anisotropically by subjecting it to noises with different strengths along different spatial directions. We show that the escape time can largely be tuned by the anisotropic driving. While the escape process becomes anisotropic due to the two different noises, the spatial symmetry is restored in the limit of large magnetic fields. This is attributed to the Lorentz force induced coupling between the spatial degrees of freedom which makes the difference between two noises irrelevant at high magnetic fields. The theoretical predictions are verified by Brownian dynamics simulations. In principle, our predictions can be tested by experiments with a Brownian gyrator in the presence of a magnetic field.

cond-mat.stat-mech↗

arXiv2021

Brownian magneto-gyrator as a tunable microengine

A Brownian particle performs gyrating motion around a potential energy minimum when subjected to thermal noises from two different heat baths. Here, we propose a magneto-gyrator made of a single charged Brownian particle that is steered by an external magnetic field. Key properties, such as the direction of gyration, the torque exerted by the engine on the confining potential and the maximum power delivered by the microengine can be tuned by varying the strength and direction of the applied magnetic field. Further tunability is obtained by rotating the potential in the plane perpendicular to the direction of the magnetic filed. We show that in this generic scenario, the microengine can be stalled and even reversed by the magnetic field. Finally, we highlight a property of the magneto-gyrator that has no counterpart in the overdamped approximation--the heat loss from the hot to cold bath requires explicit knowledge of the mass of the particle. Consequently, the efficiency of the microengine is mass-dependent even in the overdamped limit.

cond-mat.stat-mech↗