arXiv subjects

Holger Merlitz

Publications and source records attributed to Holger Merlitz.

16 recordsLinked to original sources

arXiv2025

Positive Feedback Drives Sharp Swelling of Polymer Brushes near Saturation

We resolve the Schr\"{o}der 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 $\chi$ 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↗

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↗

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↗

arXiv2020

Chemotaxis of cargo-carrying self-propelled particles

Active particles with their characteristic feature of self-propulsion are regarded as the simplest models for motility in living systems. The accumulation of active particles in low activity regions has led to the general belief that chemotaxis requires additional features and at least a minimal ability to process information and to control motion. We show that self-propelled particles display chemotaxis and move into regions of higher activity, if the particles perform work on passive objects, or cargo, to which they are bound. The origin of this cooperative chemotaxis is the exploration of the activity gradient by the active particle when bound to a load, resulting in an average excess force on the load in the direction of higher activity. Using a minimalistic theoretical model, we capture the most relevant features of these active-passive dimers and in particular we predict the crossover between anti-chemotactic and chemotactic behaviour. Moreover we show that merely connecting active particles to chains is sufficient to obtain the crossover from anti-chemotaxis to chemotaxis with increasing chain length. Such an active complex is capable of moving up a gradient of activity such as provided by a gradient of fuel and to accumulate where the fuel concentration is at its maximum. The observed transition is of significance to proto-forms of life enabling them to locate a source of nutrients even in the absence of any supporting sensomotoric apparatus.

cond-mat.soft↗

arXiv2019

Pseudo-chemotaxis of active Brownian particles competing for food

Using Brownian dynamics simulations, the motion of active Brownian particles (ABPs) in the presence of fuel (or 'food') sources is studied. It is an established fact that within confined stationary systems, the activity of ABPs generates density profiles that are enhanced in regions of low activity, which is generally referred to as 'anti-chemotaxis'. We demonstrate that -- contrary to common believes -- in non-stationary setups, emerging here as a result of short fuel bursts, our model ABPs do instead exhibit signatures of chemotactic behavior. In direct competition with inactive, but otherwise identical Brownian particles (BPs), the ABPs are shown to fetch a larger amount of food. From a biological perspective, the ability to turn active would, despite of the absence of sensoric devices, encompass an evolutionary advantage.

physics.bio-ph↗

arXiv2019

Lorentz forces induce inhomogeneity and fluxes in active systems

We consider the nonequilibrium dynamics of a charged active Brownian particle in the presence of a space dependent magnetic field. It has recently been shown that the Lorentz force induces a particle flux perpendicular to density gradients, thus preventing a diffusive description of the dynamics. Whereas a passive system will eventually relax to an equilibrium state, unaffected by the magnetic field, an active system subject to a spatially varying Lorentz force settles into a nonequilibrium steady state characterized by an inhomogeneous density and divergence-free bulk fluxes. A macroscopic flux of charged active particles is induced by the gradient of the magnetic field only and does not require additional symmetric breaking such as density or potential gradients. This stands in marked contrast to similar phenomena in condensed matter such as the classical Hall effect. In a confined geometry we observe circulating fluxes, which can be reversed by inverting the direction of the magnetic field. Our theoretical approach, based on coarse-graining of the Fokker-Planck equation, yields analytical results for the density, fluxes, and polarization in the steady state, all of which are validated by direct computer simulation. We demonstrate that passive tracer particles can be used to measure the essential effects of the Lorentz force on the active particle bath, and we discuss under which conditions the effects of the flux could be observed experimentally.

cond-mat.soft↗

arXiv2018

Linear response approach to active Brownian particles in time-varying activity fields

In a theoretical and simulation study, active Brownian particles (ABPs) in three-dimensional bulk systems are exposed to time-varying sinusoidal activity waves that are running through the system. A linear response (Green-Kubo) formalism is applied to derive fully analytical expressions for the torque-free polarization profiles of the particles. The activity waves induce fluxes that strongly depend on the particle size and may be employed to de-mix mixtures of ABPs or to drive the particles into selected areas of the system. Three-dimensional Langevin dynamics simulations are carried out to verify the accuracy of the linear response formalism, which is shown to work best when the particles are small (i.e., highly Brownian) or operating at low activity levels.

cond-mat.soft↗

arXiv2017

Pseudochemotaxis in inhomogeneous active Brownian systems

We study dynamical properties of confined, self-propelled Brownian particles in an inhomogeneous activity profile. Using Brownian dynamics simulations, we calculate the probability to reach a fixed target and the mean first passage time to the target of an active particle. We show that both these quantities are strongly influenced by the inhomogeneous activity. When the activity is distributed such that high-activity zone is located between the target and the starting location, the target finding probability is increased and the passage time is decreased in comparison to a uniformly active system. Moreover, for a continuously distributed profile, the activity gradient results in a drift of active particle up the gradient bearing resemblance to chemotaxis. Integrating out the orientational degrees of freedom, we derive an approximate Fokker-Planck equation and show that the theoretical predictions are in very good agreement with the Brownian dynamics simulations.

cond-mat.soft↗

arXiv2014

Maximal rectification ratios for bi-segment thermal rectifiers

We study bi-segment thermal rectifiers whose forward heat fluxes are greater than reverse counterparts. Presently, a shortcoming of thermal rectifiers is that the rectification ratio, namely the forward flux divided by the reverse flux, remains too small for practical applications. In this study, we have managed to discover and theoretically derive the ultimate limit of such ratios, which are validated by numerical simulations, experiments, and micro-scale Hamiltonian-oscillator analyses. For rectifiers whose thermal conductivities are linear with the temperature, this limit is simply a numerical value of 3. For those whose conductivities are nonlinear with temperatures, the maxima equal $\kappa_{max}/\kappa_{min}$, where the two extremes denote values of the solid segment materials that can be possibly found or fabricated within a reasonable temperature range on earth. Recommendations for manufacturing high-ratio rectifiers are also given with examples.

physics.comp-ph↗

arXiv2009

How proteins squeeze through polymer networks: a Cartesian lattice study

In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense networks are created by a combined version of the bond fluctuation method and a Metropolis Monte Carlo algorithm. Semidilute behaviour of the dense chain networks is shown. By comparing diffusion of particles in a static and a dynamical chain network, we demonstrate that chain diffusion does not alter the diffusion process of small particles. However, we prove that a dynamical network facilitates the transport of large particles. By weighting the mean square displacement trajectories of particles in the static chain network data from the dynamical network can be reconstructed. Additionally, it is shown that subdiffusive behaviour of particles on short time scales results from trapping processes in the crowded environment of the chain network. In the presented model a protein with 30 nm diameter has an effective diffusion coefficient of 1.24E-11 m^2/s in a chromatin fiber network.

physics.bio-ph↗

arXiv2008

Nano-scale brushes: How to build a smart surface coating

Via computer simulations, we demonstrate how a densely grafted layer of polymers, a {\it brush}, could be turned into an efficient switch through chemical modification of some of its end-monomers. In this way, a surface coating with reversibly switchable properties can be constructed. We analyze the fundamental physical principle behind its function, a recently discovered surface instability, and demonstrate that the combination of a high grafting density, an inflated end-group size and a high degree of monodispersity are conditions for an optimal functionality of the switch.

cond-mat.soft↗

arXiv2007

Modelling diffusional transport in the interphase cell nucleus

In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles, a random walk chain model, and a self avoiding random walk chain model with persistence length. By comparing a discrete and a continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter particle diffusion. The influence of the 3D geometry of the fiber network on the particle diffusion is investigated in detail, while varying occupation volume, chain length, persistence length and walker size. It is shown that adjacency of the monomers, the excluded volume effect incorporated in the self avoiding random walk model, and, to a lesser extent, the persistence length, affect particle diffusion. It is demonstrated how the introduction of the effective chain occupancy, which is a convolution of the geometric chain volume with the walker size, eliminates the conformational effects of the network on the diffusion, i.e., when plotting the diffusion coefficient as a function of the effective chain volume, the data fall onto a master curve.

physics.bio-ph↗

arXiv2006

Facilitated diffusion of DNA-binding proteins: Simulation of large systems

The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be calibrated in numerical simulations inside a test system of moderate size. Once this is done, reaction times of systems of arbitrary dimensions are derived by extrapolation, with an accuracy of 10 to 15 percent. The achieved speed up, when compared to explicit simulations of the reaction process, is increasing proportional to the extrapolated volume of the cell.

physics.bio-ph↗

arXiv2005

Facilitated diffusion of DNA-binding proteins

The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is verified by numerical simulations. The results confirm that the unspecific binding of protein to DNA, combined with sliding, is capable to reduce the reaction times significantly.

physics.bio-ph↗

arXiv2005

Facilitated diffusion of DNA-binding proteins: Efficient simulation with the method of excess collisions (MEC)

In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing modes, a free diffusion and a DNA-sliding mode, to search for its specific binding site in the center of the cell. There is no need for a straightforward simulation of this process. Instead, an alternative and exact approach is shown to be essentially faster than explicit random-walk simulations. The speed-up of this novel simulation technique is rapidly growing with system size.

physics.bio-ph↗

arXiv2004

Application of Relativistic Coupled-cluster Theory to Heavy Atomic Systems with Strongly Interacting Configurations: Hyperfine Interactions in $^{207}Pb^+$

This work presents a first time accurate calculation of the magnetic dipole hyperfine structure constants for the ground state and some low-lying excited states of Pb$^+$. By comparing different levels of approximation with experimental results, we demonstrate the importance of correlation effects which reach beyond lower order relativistic many body perturbation theory. Employing relativistic coupled-cluster theory we obtain a quantitative understanding of the core-polarization and correlation effects inherent in this system and observe completely different trends compared to $Ba^+$.

physics.atom-ph↗