Article
Physics, Multidisciplinary
Luca Angelani
Summary: Complex or hostile environments can hinder the movement capabilities of diffusive particles or active swimmers, leading to their immobilization. This study analyzes the dynamics of active particles in trapping regions and provides expressions for the probability distribution and mean trapping times of blocked particles. Different sizes of trapping regions are considered, from infinite to semi-infinite and finite intervals.
Article
Chemistry, Multidisciplinary
Jiabin Luan, Peter F. Kuijken, Wen Chen, Danni Wang, Levy A. Charleston, Daniela A. Wilson
Summary: Biodegradable streamlined alginate hydrogel micromotors with a teardrop shape are fabricated by microfluidics, enabling high-throughput production and precise variation in size. By tuning the localization regions of catalysts, the micromotors exhibit improved propulsion efficiency and achieve distinct motion patterns.
Article
Physics, Fluids & Plasmas
Naftali R. Smith, Pierre Le Doussal, Satya N. Majumdar, Gregory Schehr
Summary: This paper investigates an overdamped run-and-tumble particle in two dimensions with self-propulsion that stochastically rotates. By changing the coordinates, the problem is decomposed into two statistically independent one-dimensional problems, enabling the exact solutions for the particle's position distribution and steady-state distribution to be found.
Article
Mechanics
Luca Angelani
Summary: This paper investigates planar run-and-tumble walks with orthogonal directions of motion. The problem is formulated with generic transition probabilities among the orientational states. The study focuses on the symmetric case and provides general expressions for the probability distribution function, mean-square displacement, and effective diffusion constant. The paper also discusses the cases of alternate/forward and isotropic/backward motion, as well as cyclic motion, observing reduced (enhanced) effective diffusivity compared to standard 2D active motion.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Mechanics
Derek Frydel
Summary: This paper investigates the four-state run-and-tumble particle model at zero temperature and proposes an enhanced model by increasing the number of discrete velocities. The analysis reveals that fast particles tend to accumulate at the walls while slow particles deplete gradually.
Article
Physics, Fluids & Plasmas
Pierre Le Doussal, Satya N. Majumdar, Gregory Schehr
Summary: This study focuses on the stationary bound state formed by two interacting identical run-and-tumble particles (RTPs) in one dimension. The distribution of the relative coordinate y reaches a steady state characterized by the solution of a second-order differential equation. Explicit formulas for the stationary probability of y under different interaction potentials are obtained.
Article
Physics, Multidisciplinary
Luca Angelani
Summary: This study analyzes the behavior of run-and-tumble particles in one-dimensional finite domains under generic boundary conditions. The unified formulation allows for the treatment of various different boundary conditions and provides a general expression for the mean exit time.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2023)
Article
Physics, Fluids & Plasmas
Sergei Fedotov, Daniel Han, Alexey O. Ivanov, Marco A. A. da Silva
Summary: This paper introduces a run-and-tumble model with self-reinforcing directionality and rests, and derives a hyperbolic partial differential equation for the probability density of random-walk position. The research finds that the transition between superdiffusion and diffusion caused by the addition of a rest state depends on both the parameter representing the strength of self-reinforcement and the ratio between mean running and resting times.
Article
Mechanics
Derek Frydel
Summary: This study focuses on the three-dimensional RTP model in a harmonic trap and derives the recurrence relation for generating moments of a stationary distribution. These moments are then used to recover the stationary distribution.
Article
Physics, Fluids & Plasmas
Derek Frydel
Summary: This work investigates the entropy production rate, Pi, of the run-and-tumble model and focuses on its scaling with the persistence time tau. It is found that, in the limit of tau approaching infinity, Pi tends to zero, indicating equilibrium; while in the limit of tau approaching zero, Pi reaches its optimal value, indicating a departure from equilibrium.
Article
Physics, Multidisciplinary
Pascal Grange, Xueqi Yao
Summary: The study proposes a model of run-and-tumble particles on a line with a fertile site, where new particles are generated until a change in direction occurs. The system maintains parity invariance and the motion equations can be solved using density. At large time scales, the density of particles grows exponentially, depending on the fertility function and rate. The total density of particles reaches a stable state, with a local minimum at the fertile site.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Physics, Multidisciplinary
Prashant Singh, Saikat Santra, Anupam Kundu
Summary: This paper investigates the extreme value statistics of a run and tumble particle (RTP) in one dimension until its first passage to the origin. The joint distribution of the maximum displacement and the time at which this maximum is achieved is computed using the exact time-dependent propagators. The marginal distributions of the maximum displacement and the time are separately studied, and their asymptotic forms are found to depend on the initial conditions.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Physics, Multidisciplinary
Ziluo Zhang, Gunnar Pruessner
Summary: In this work, the motion of free run and tumble particles in arbitrary dimensions is described using Doi-Peliti field theory. The mean squared displacement and entropy production at stationarity are calculated, and the field theory of free active Brownian particles in two dimensions is derived for comparison.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Physics, Multidisciplinary
Christian Maes, Kasper Meerts, Ward Struyve
Summary: This article discusses the problem of considering run-and-tumble particles (such as bacteria) in a quantum mechanical relation, and discusses their motion characteristics and trajectories, as well as their dependence on spin direction and spacetime parameters.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2022)
Article
Physics, Multidisciplinary
Prashant Singh, Anupam Kundu, Satya N. Majumdar, Hendrik Schawe
Summary: In this study, the statistics of the convex hull for a single run-and-tumble particle (RTP) in two dimensions were investigated, considering two different statistical ensembles. Exact analytical expressions for the mean area were obtained, revealing scaling behavior in different time regimes and linear growth with the total number of tumbles.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Correction
Polymer Science
David Beyer, Jonas Landsgesell, Pascal Hebbeker, Oleg Rud, Raju Lunkad, Peter Kosovan, Christian Holm
Article
Polymer Science
Jonas Landsgesell, David Beyer, Pascal Hebbeker, Peter Kosovan, Christian Holm
Summary: This study investigates the swelling properties of weak polyelectrolyte gels using a hierarchy of models. The results show that particle-based models are the most accurate in predicting gel swelling, but field-based models can also reasonably explain the experimental trends.
Article
Biochemistry & Molecular Biology
Mariano E. Brito, Sofia E. Mikhtaniuk, Igor M. Neelov, Oleg V. Borisov, Christian Holm
Summary: The design of nanoassemblies can be achieved by adjusting the strength of hydrophobic interactions in block copolymers. These supramolecular aggregates have attracted attention in drug delivery and imaging due to their tunable properties and scalable production. In this study, we investigated the micellization process of linear-dendritic block copolymers to understand the effect of branching on micellar properties. We found that excluded volume interactions strongly influence the aggregation and charge of micelles at higher degrees of branching and for shorter polymer chains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Oleg V. V. Shavykin, Sofia E. E. Mikhtaniuk, Emil I. I. Fatullaev, Igor M. M. Neelov, Frans A. M. Leermakers, Mariano E. E. Brito, Christian Holm, Oleg V. V. Borisov, Anatoly A. A. Darinskii
Summary: In this article, the micellization of hybrid molecules consisting of one polylysine dendron with charged end groups and several linear hydrophobic tails attached to its root was studied using the numerical self-consistent field method of Scheutjens-Fleer. The focus was on the formation of spherical micelles and the determination of the parameters for their appearance. The relationship between the size and structure of spherical micelles and the length and number of hydrophobic tails, as well as the number of dendron generations, was established. The relationship between the structure of hybrid molecules and the electrostatic properties of the resulting micelles was also investigated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Le Qiao, Kai Szuttor, Christian Holm, Gary W. Slater
Summary: We propose a new concept for separating DNA molecules based on their contour length, using a combination of nanofluidic ratchet, nanopore translocation, and pulsed fields. Through simulations, we demonstrate that pulsed field sequences can selectively translocate short chains, effectively transforming the nanopore process into a low pass molecular filter. Asymmetric pulses are also shown to enhance device efficiency. This process can be performed with multiple pores in parallel and integrated into nanopore sequencing devices, increasing its potential utility.
Article
Chemistry, Physical
Patrick Kreissl, Christian Holm, Rudolf Weeber
Summary: Magnetic nanoparticles couple to polymeric environments through various mechanisms, including van der Waals, steric, hydrodynamic, and electrostatic forces. This leads to interesting effects and potential applications, although the details of the coupling are often unknown. Previous work has shown that hydrodynamic coupling alone can explain observed trends in magnetic AC susceptibility spectra for spherical particles. Now, this publication focuses on the interplay of steric and hydrodynamic interactions in non-spherical particles and their coupling to a polymer suspension.
Article
Chemistry, Physical
Simon Gravelle, David Beyer, Mariano Brito, Alexander Schlaich, Christian Holm
Summary: NMR relaxometry is a powerful experimental approach for studying dynamic processes in soft matter systems. All-atom simulations provide detailed insights but are limited in modeling long polymer chains or hydrogels, while coarse-graining can overcome this limitation but sacrifices atomistic details. This study investigates the dipolar relaxation rates of a PEG-H2O mixture at both all-atom and coarse-grained levels, revealing that the coarse-grained results exhibit similar trends but with a systematic offset due to the absence of intramonomer component and imprecise positioning of spin carriers. The offset can be corrected by reconstructing atomistic details from the coarse-grained trajectories.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Simon Gravelle, Sabina Haber-Pohlmeier, Carlos Mattea, Siegfried Stapf, Christian Holm, Alexander Schlaich
Summary: Through nuclear magnetic relaxation dispersion measurements, we explore the dynamic properties of water within salt crusts, specifically sodium chloride (NaCl) and sodium sulfate (Na2SO4). Our findings indicate that sodium sulfate salt crusts exhibit a higher frequency-dependent relaxation time T (1) than sodium chloride salt crusts. Molecular dynamics simulations further demonstrate that pore size and salt concentration significantly affect the value of T (1). These simulations shed light on the interplay between ion adsorption, water structure near the interface, and dispersion of T (1) at low frequency, which can be attributed to adsorption-desorption events.
Article
Chemistry, Multidisciplinary
Samuel Tovey, Fabian Zills, Francisco Torres-Herrador, Christoph Lohrmann, Marco Brueckner, Christian Holm
Summary: This article introduces a post-processing tool called MDSuite, which is developed in Python and combines state-of-the-art computing technologies such as TensorFlow with modern data management tools like HDF5 and SQL. It provides a fast, scalable, and accurate data processing engine for particle simulations. The software currently offers 17 calculators for the computation of various properties, and it also supports the rapid implementation of new calculators or file-readers. The Python front-end provides a familiar interface for many users in the scientific community and has a mild learning curve for the inexperienced.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Chemistry, Physical
Alexander Schlaich, Sandeep Tyagi, Stefan Kesselheim, Marcello Sega, Christian Holm
Summary: The DLVO theory is a landmark in colloidal particle modeling, and can be used to solve the interaction problem between charged colloids. Our numerical results match the analytical predictions and provide a reinterpretation of previous molecular dynamics simulations.
EUROPEAN PHYSICAL JOURNAL E
(2023)
Article
Chemistry, Physical
David Beyer, Christian Holm
Summary: We propose a Monte-Carlo method for simulating a polymeric phase with a weak polyelectrolyte coupled to a reservoir with fixed pH, salt concentration, and total concentration of a weak polyprotic acid. The method extends the grand-reaction method by Landsgesell et al. [Macromolecules 53, 3007-3020 (2020)], enabling simulations of polyelectrolyte systems coupled to more complex reservoirs. We also generalize the chemical potential tuning algorithm of Miles et al. [Phys. Rev. E 105, 045311 (2022)] to set the input parameters for the desired reservoir composition.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Jie Yang, Svyatoslav Kondrat, Cheng Lian, Honglai Liu, Alexander Schlaich, Christian Holm
Summary: In this study, the influence of solvent on the structure and ionic screening of electrolytes under slit confinement and in contact with a reservoir was investigated using classical density functional theory. It was found that spatially resolving solvent molecules is essential for understanding the ion structure, excess ion adsorption, and pressure exerted on the walls. While there were only moderate differences observed in the pressure oscillations and decay lengths based on the ion diameter and Debye length, the crossover to the hard-core-dominated regime depended sensitively on the relative permittivity, ion concentration, and other factors.
PHYSICAL REVIEW LETTERS
(2023)
Article
Computer Science, Artificial Intelligence
Samuel Tovey, Sven Krippendorf, Konstantin Nikolaou, Christian Holm
Summary: This work introduces two collective variables, entropy and trace of the empirical neural tangent kernel, and empirically analyzes their correlation with the performance and generalization of neural networks. The framework is also applied to the problem of optimal data selection and shows that random network distillation can outperform random selection.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2023)
Article
Chemistry, Physical
Henrik Jaeger, Alexander Schlaich, Jie Yang, Cheng Lian, Svyatoslav Kondrat, Christian Holm
Summary: The emergence of anomalously large screening lengths at high ion concentrations in room-temperature ionic liquids and concentrated electrolytes, known as underscreening, challenges classical theories and our understanding of electrostatic correlations. Despite extensive experimental, analytical, and simulation efforts, the origin of this long-range screening remains elusive.
FARADAY DISCUSSIONS
(2023)
Article
Chemistry, Physical
Christoph Lohrmann, Christian Holm
Summary: Studying the initial stages of biofilm formation is crucial for understanding the interactions between bacteria, fluid, and geometry. This study presents a new numerical model that takes into account the motion of bacteria and the growth of biofilm, as well as the influence of external flow.
