Article
Mechanics
Tristan Gautie, Naftali R. Smith
Summary: This study revisits the Ferrari-Spohn model of a Brownian bridge conditioned to avoid a moving wall, pushing the system into a large-deviation regime. The model is extended to an arbitrary number of non-crossing Brownian bridges, with the joint distribution of the distances of the particles from the wall obtained in terms of the determinant of an N x N matrix. The distribution coincides with that of noninteracting fermions trapped by a linear potential with a hard wall.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Chemistry, Physical
Bart Vorselaars
Summary: We introduce Langevin sampling algorithms for field-theoretic simulations (FTSs) of polymers, which are significantly more efficient than previously used Brownian dynamics algorithm, smart Monte Carlo (SMC) algorithm, and simple Monte Carlo (MC) algorithm. The Leimkuhler-Matthews method and the BAOAB method show great improvement in efficiency. In addition, the FTS allows for an improved MC algorithm based on the Ornstein-Uhlenbeck process (OU MC), which outperforms SMC. The efficiency of the sampling algorithms also depends on the system size, and the Monte Carlo algorithms mentioned do not scale well with larger sizes.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Astronomy & Astrophysics
Jen-Tsung Hsiang, Bei-Lok Hu
Summary: This study reexamines the motion of a point charge emitting radiation in an electromagnetic field from the perspective of non-Markovian dynamics. By casting the problem as the non-Markovian dynamics of a Brownian oscillator in a supra-Ohmic environment, it is found that there is no need for a second derivative initial condition and no preacceleration.
Article
Physics, Fluids & Plasmas
Maria de Jesus Martinez-Lopez, Jose Luis Arauz-Lara
Summary: The motion of colloidal species on an out-of-thermal equilibrium surface was experimentally studied using optical microscopy. Water droplets of submicrometer sizes, spontaneously formed at the interface between water and oil, were observed to move and grow without showing anomalous diffusion.
Article
Chemistry, Physical
Yashraj M. Wani, Penelope Grace Kovakas, Arash Nikoubashman, Michael P. Howard
Summary: We studied self-diffusion and sedimentation in colloidal suspensions of nearly hard spheres using the MD+MPCD simulation method. The results suggest that MD+MPCD provides a reasonable description of hydrodynamic interactions in colloidal suspensions and can be conveniently extended to more complex shapes.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Condensed Matter
J. Galen Wang, Roseanna N. Zia
Summary: Persistent dynamics in colloidal glasses suggest a non-equilibrium driving force for structural relaxation during glassy aging, with osmotic pressure identified as a potential driving force. Quenching a polydisperse hard-sphere colloidal liquid into the putative glass region allows for the osmotic pressure to drive redistribution of coordination number and interparticle voids, ultimately smoothing structural heterogeneity with age. Osmotic pressure plays a crucial role in driving structural rearrangements responsible for vitrification and glassy age-relaxation, with the system eventually relaxing toward a metastable state.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2021)
Article
Multidisciplinary Sciences
N. Levernier, T. Mendes, O. Benichou, R. Voituriez, T. Guerin
Summary: Persistence plays a crucial role in random processes, but calculating persistence exponents for non-Markovian systems is difficult. This study introduces a theoretical framework that determines the persistence exponents of Gaussian non-Markovian processes with non-stationary dynamics.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Camilla M. Kjeldbjerg, John F. Brady
Summary: Researchers have found that active Brownian particles distribute non-homogeneously near surfaces and accumulate at no-flux surfaces due to their persistent swimming. Additionally, it has been observed that two parallel plates in a dilute bath of ABPs experience a Casimir effect and attract each other.
Article
Mechanics
Alain Mazzolo, Cecile Monthus
Summary: This article introduces the application of local time in conditioned processes. By constructing various conditioned processes involving the final local time A* (T), constrained stochastic trajectories are generated for three diffusions with different recurrence/transience properties.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Chemistry, Physical
Tetsuro Nagai, Akira Yoshimori, Susumu Okazaki
Summary: This study investigates a series of new Monte Carlo transition probabilities that can simulate molecular trajectories satisfying the diffusion equation. The results show good agreement with the numerical solution. The method is useful for studying long-distance transport of molecules in heterogeneous systems and many-particle dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Camilla M. Kjeldbjerg, John F. Brady
Summary: Passive Brownian particles distribute evenly between porous medium and fluid reservoir, while active particles tend to accumulate near boundaries and preferentially partition into the porous medium. The study explores the behavior of active swimmers partitioning into a porous medium from a bulk fluid reservoir, showing oscillatory behavior at short times and steady state concentration partitioning at longer times.
Article
Mechanics
Maria Refinetti, Sebastian Goldt
Summary: Autoencoders are simple neural networks that can be used for unsupervised learning and studying feature extraction. This study focuses on the dynamics of feature learning in non-linear, shallow autoencoders and derives equations that describe the generalization dynamics. The analysis reveals important factors that affect the learning process.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2023)
Article
Physics, Multidisciplinary
Magnus G. Skou, Thomas G. Skov, Nils B. Jorgensen, Kristian K. Nielsen, Arturo Camacho-Guardian, Thomas Pohl, Georg M. Bruun, Jan J. Arlt
Summary: Advancing our understanding of non-equilibrium phenomena in quantum many-body systems remains a major challenge in physics. The experimental observation of the non-equilibrium dynamics of a quantum impurity immersed in a bosonic environment reveals a systematic picture of polaron formation and provides a link between few-body processes and many-body dynamics. The measurements demonstrate universal dynamical behavior in interacting many-body systems and offer new pathways to study non-equilibrium quantum phenomena.
Article
Chemistry, Physical
Thorsten Prustel, Martin Meier-Schellersheim
Summary: This study focused on computational models of reaction-diffusion systems commonly found in cellular signaling pathways, and introduced an approach that allows for the reconstruction of entire molecular trajectories after a simulated time step, avoiding the need for inefficient draws from non-standard distributions. This method enables highly accurate stochastic simulations for system sizes that would be prohibitively costly to simulate with conventional Green's function based methods.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Thermodynamics
Irina A. Graur, Marina A. Batueva, Moritz Wolf, Elizaveta Ya. Gatapova
Summary: This article conducts numerical simulations of monatomic vapor condensation on its liquid phase using three different methods. The results show good agreement among these methods for monatomic gases. The Moment Method is found to have great potential for efficient estimation of condensation fluxes while respecting the conservation of mass, momentum, and energy. The study also discusses the presence and effects of an inverted temperature gradient during the condensation process, and proposes a methodology for extracting the condensation coefficient based on the Moment Method results.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2022)
Article
Multidisciplinary Sciences
David B. Brueckner, Nicolas Arlt, Alexandra Fink, Pierre Ronceray, Joachim O. Raedler, Chase P. Broedersz
Summary: The study found that the interactions between noncancerous cells are mainly described by repulsion and friction interactions, while cancerous cells exhibit attraction and antifriction interactions. These interaction behaviors were validated in experiments and may provide a unifying theoretical description for diverse cellular interaction behaviors of different cell types.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Joris J. B. Messelink, Muriel C. F. van Teeseling, Jacqueline Janssen, Martin Thanbichler, Chase P. Broedersz
Summary: The study develops a fully data-driven method to extract single-cell 3D chromosome conformations from Hi-C experiments on Caulobacter crescentus, revealing the order and variability of bacterial chromosome organization, such as long-ranged two-point axial correlations on large genomic scales and chromosome extensions correlating with transcriptional and loop extrusion activity on smaller scales. This approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.
NATURE COMMUNICATIONS
(2021)
Article
Biophysics
Themistoklis Zisis, David B. Brueckner, Tom Brandstaetter, Wei Xiong Siow, Joseph d'Alessandro, Angelika M. Vollmar, Chase P. Broedersz, Stefan Zahler
Summary: This study utilizes theoretical modeling and experimental observations to investigate the impact of intercellular interactions on collective spreading behavior, specifically focusing on the role of E- and N-cadherin junctions. The research reveals that inhibiting these junctions decreases colony spreading and velocity, without affecting the correlation strength of neighboring cell velocities.
BIOPHYSICAL JOURNAL
(2022)
Article
Physics, Multidisciplinary
Pierre Ronceray, Sheng Mao, Andrej Kosmrlj, Mikko P. Haataja
Summary: In this study, the researchers investigate the mechanical interactions between phase-separated liquid condensates and surrounding elastic networks in cells. Through theoretical analysis, they propose the existence of three thermodynamically stable droplet phases, including macroscopic droplets that either cavitate or permeate the network, and mesh-size-limited microdroplets. The study also suggests the possibility of yet-unobserved droplet phases in the cytoplasm and nucleoplasm.
Article
Physics, Multidisciplinary
Pierre Ronceray, Yaojun Zhang, Xichong Liu, Ned S. Wingreen
Summary: Multivalent associative proteins are essential for phase separation in intracellular liquid condensates. This study investigates the internal dynamics of bond-network condensates composed of two complementary proteins through scaling analysis and molecular dynamics. The findings reveal that when the stoichiometry is balanced, relaxation significantly slows down due to a lack of alternative binding partners, which strongly influences bulk diffusivity, viscosity, and mixing. This provides an experimental means to test the prediction.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Anna E. C. Meijering, Kata Sarlos, Christian F. Nielsen, Hannes Witt, Janni Harju, Emma Kerklingh, Guus H. Haasnoot, Anna H. Bizard, Iddo Heller, Chase P. Broedersz, Ying Liu, Erwin J. G. Peterman, Ian D. Hickson, Gijs J. L. Wuite
Summary: In this study, a workflow based on optical trapping and manipulation is introduced to investigate the organization of human chromosomes. The research reveals that chromosomes exhibit nonlinear stiffening behavior under increasing mechanical load and introduces a hierarchical worm-like chain model to explain this anomalous stiffening.
Editorial Material
Multidisciplinary Sciences
Chase P. Broedersz, Pierre Ronceray
Summary: This paper discusses how the Jarzynski equality updates the second law of thermodynamics by extending the physics of transformations from steam engines to molecular motors.
Article
Chemistry, Physical
Haiyang Jia, Johannes Flommersfeld, Michael Heymann, Sven K. Vogel, Henri G. Franquelim, David B. Bruckner, Hiromune Eto, Chase P. Broedersz, Petra Schwille
Summary: This study presents a method of creating protein-based robotic structures using 3D printing technology, which can undergo micrometre-scale shape-morphing activity through the actuation of exoskeleton-like molecular motor assemblies. By utilizing an actomyosin cortex-like force production, low complexity motor arrangements can be achieved in a contractile meshwork that can be locally activated. This design allows for easy connection and assembly of micro-3D printed modules into larger structures, enabling mechanical work on a larger scale.
Correction
Multidisciplinary Sciences
Anna E. C. Meijering, Kata Sarlos, Christian F. Nielsen, Hannes Witt, Janni Harju, Emma Kerklingh, Guus H. Haasnoot, Anna H. Bizard, Iddo Heller, Chase P. Broedersz, Ying Liu, Erwin J. G. Peterman, Ian D. Hickson, Gijs J. L. Wuite
Article
Physics, Multidisciplinary
David B. Brueckner, Matthew Schmitt, Alexandra Fink, Georg Ladurner, Johannes Flommersfeld, Nicolas Arlt, Edouard Hannezo, Joachim O. Raedler, Chase P. Broedersz
Summary: This research develops a model for protrusion and polarity dynamics in confined cell migration using data-driven inference and a mechanistic bottom-up approach. The study reveals that cellular dynamics adapt to confining geometries through a switch in polarity dynamics, driving the migration of the cell through constrictions.
Article
Multidisciplinary Sciences
Haiqian Yang, Estelle Berthier, Chenghai Li, Pierre Ronceray, Yu Long Han, Chase P. Broedersz, Shengqiang Cai, Ming Guo
Summary: Nonlinear stiffening is a widespread property of biopolymers in the extracellular matrices, and cells can locally stretch and stiffen the surrounding matrix through a spindle-like shape. By using optical tweezers, we studied the force-displacement response to localized monopole forces and proposed a scaling argument to characterize the stiffened region in the matrix.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Tom Brandstaetter, David B. Brueckner, Yu Long Han, Ricard Alert, Ming Guo, Chase P. Broedersz
Summary: Cell migration in rotating spherical tissues exhibits a collective mode with a single-wavelength velocity wave, which is accompanied by a supracellular flow pattern featuring topological defects. This collective migration mode arises from the effect of curvature on the active flocking behavior of cells on a spherical surface.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Fluids & Plasmas
Grzegorz Gradziuk, Gabriel Torregrosa, Chase P. Broedersz
Summary: This article analyzes the effects of temporal correlations in noise on measures of irreversibility and extends the theoretical framework for white-noise-driven systems to colored noise.
Article
Physics, Fluids & Plasmas
Sihan Chen, Chase P. Broedersz, Tomer Markovich, Fred C. MacKintosh
Summary: The mechanics of living cells are largely determined by the cytoskeleton, a biopolymer network with transient crosslinkers allowing for stress relaxation over time. Additionally, internal stress in these networks is caused by the presence of molecular motors. A theoretical model using mode-dependent mobility was proposed to explain the stress relaxation in such prestressed transient networks, showing good agreement with experimental data.