Article
Mechanics
Sutapa Mukherji
Summary: The study investigates the cargo transport process in cells and reveals the hindrance caused by the association or dissociation of motor proteins. A model with particle annihilation is proposed, and boundary-induced phase transitions are observed. The phase diagram is predicted based on the analysis of mean-field solutions and the phase portrait of the differential equation.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Physics, Fluids & Plasmas
Hiroki Yamamoto, Shingo Ichiki, Daichi Yanagisawa, Katsuhiro Nishinari
Summary: This paper proposes a two-lane model with interactions between the lanes and investigates both bidirectional and unidirectional flows. Theoretical expressions for the global density of the system in the steady state are obtained through mean-field analyses, and it is found that the (2 x 2)-cluster mean-field analysis approximates the simulation results well. The phenomena are explained qualitatively through a simple analysis of correlations. These findings provide informative suggestions for actual traffic systems.
Article
Mathematics, Interdisciplinary Applications
Bipasha Pal, Arvind Kumar Gupta
Summary: We investigate a totally asymmetric simple exclusion process with Langmuir kinetics and conservation of total particle number controlled by filling factor mu. Crowding of the reservoir is taken into account in addition to the entry and exit of particles. We use mean-field approximation to express density profiles and obtain phase diagrams in the alpha - beta parameter space, showing changes in topology near mu = 1. The interplay of reservoir crowding and Langmuir kinetics leads to a novel back-and-forth transition feature. Theoretical phase boundaries and density profiles are validated through extensive Monte Carlo simulations.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Physics, Multidisciplinary
Bo Tian, Wan-Qiang Wen, A-Min Li, Ping Xia
Summary: This paper investigates two-lane asymmetric simple exclusion processes (ASEPs) with an intersection. Monte Carlo simulations are conducted to study the system's behavior. The results show that there are three symmetric phases and no spontaneous symmetry breaking (SSB) in the system. Initially, a simple mean field approach is used to analyze the system, but it deviates from the simulation results, especially for small values of the parameter p. Therefore, a cluster mean field analysis is conducted, considering the correlation of five sites. The analysis demonstrates that densities of the two upstream segments are equal, indicating the absence of SSB. The cluster mean field analysis performs better than the simple mean field analysis.
Article
Statistics & Probability
Nina Gantert, Evita Nestoridi, Dominik Schmid
Summary: In this study, the mixing times of the symmetric and asymmetric simple exclusion process are examined when particles are allowed to enter and exit at the endpoints. Depending on the rates in the bulk and the entering and exiting rates, the process exhibits pre-cutoff and cutoff behaviors. The main contribution of this study is investigating the mixing times for the asymmetric simple exclusion process with open boundaries. It is shown that the mixing time can have a linear or exponential relationship with the size of the segment, depending on the choice of boundary parameters.
ANNALS OF APPLIED PROBABILITY
(2023)
Article
Environmental Sciences
Paraskevi Georgakaki, Georgia Sotiropoulou, Etienne Vignon, Anne-Claire Billault-Roux, Alexis Berne, Athanasios Nenes
Summary: Simulations and observations show that ice crystal formation in orographic mixed-phase clouds is influenced by seeder-feeder events from higher precipitating cloud layers and snowflake aggregation. Blowing snow and secondary ice fragment generation can enhance ice crystal number concentrations, which can be counteracted by increases in orographic precipitation.
ATMOSPHERIC CHEMISTRY AND PHYSICS
(2022)
Article
Statistics & Probability
Wlodek Bryc, Yizao Wang, Jacek Wesolowski
Summary: This paper demonstrates that the stationary measures for KPZ fixed point with Neumann boundary conditions arise as the scaling limits of height increment processes for the open asymmetric simple exclusion process.
ANNALES DE L INSTITUT HENRI POINCARE-PROBABILITES ET STATISTIQUES
(2023)
Article
Chemistry, Multidisciplinary
Akari Waragai, Taichi Nakagawa, Willie L. Hinze, Yoshitaka Takagai
Summary: The study demonstrates that a combination of sodium borohydride and ascorbic acid can synthesize urchn-shaped gold nanoparticles with controlled sizes and shapes in a short period of time, providing a new approach for the preparation of nanomaterials.
Article
Physics, Multidisciplinary
Bipasha Pal, Arvind Kumar Gupta
Summary: The study investigates a system composed of an exclusion process coupled with a reservoir, exploring the impact of limited resources on entities entering and exiting pathways in transport systems. The findings reveal rich behavior in the system, with reservoir crowding effects leading to symmetric and asymmetric phases. Even with very few particles in the system, spontaneous symmetry breaking phenomena can occur.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Statistics & Probability
M. Jara, C. Landim, K. Tsunoda
Summary: In the diffusive time-scale, weakly asymmetric exclusion processes with initial density profile as a small perturbation of a constant evolve as the solution of a viscous Burgers equation in all dimensions.
ANNALES DE L INSTITUT HENRI POINCARE-PROBABILITES ET STATISTIQUES
(2021)
Article
Chemistry, Physical
Morgan A. Perkins, Gregory S. Tschumper
Summary: This study presents the first systematic comparison of hydrogen- and halogen-bonded configurations of the HCN/HX mixed dimer. A total of eleven different minima were identified, with the relative energy of the halogen-bonded local minima becoming more competitive with the global minimum as the atomic radius of the halogen increases.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Statistics & Probability
Lina Bian, Guanjun Wang, Peng Liu
Summary: In this article, an extended mixed shock model is investigated, which considers the mutual dependence between competing soft failure and hard failure processes in a system. The model shows that the degradation of the system is influenced by both the amount of shocks and the degradation threshold. The reliability and some reliability indices of the system are obtained using stochastic process theory.
Article
Statistics & Probability
Dominik Schmid
Summary: We study the mixing times of the TASEP with open boundaries on a segment of size N. We prove that the mixing time is of order N3/2 in the maximal current phase, with logarithmic corrections. We also show that at the triple point, where the TASEP with open boundaries approaches the Uniform distribution, the mixing time is precisely of order N3/2. These findings have implications for a wide range of particle systems with maximal current.
ANNALS OF PROBABILITY
(2023)
Article
Biochemistry & Molecular Biology
Matthew R. McFarland, Corina D. Keller, Brandon M. Childers, Stephen A. Adeniyi, Holly Corrigall, Adelaide Raguin, M. Carmen Romano, Ian Stansfield
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemical Research Methods
Martin Carballo-Pacheco, Michael D. Nicholson, Elin E. Lilja, Rosalind J. Allen, Bartlomiej Waclaw
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biology
Cristina Parigini, Philip Greulich
Article
Chemistry, Physical
Matteo Paloni, Remy Bailly, Luca Ciandrini, Alessandro Barducci
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Biochemistry & Molecular Biology
Juraj Szavits-Nossan, Luca Ciandrini
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Ana Zuniga, Sarah Guiziou, Pauline Mayonove, Zachary Ben Meriem, Miguel Camacho, Violaine Moreau, Luca Ciandrini, Pascal Hersen, Jerome Bonnet
NATURE COMMUNICATIONS
(2020)
Article
Developmental Biology
Philip Greulich, Ben D. MacArthur, Cristina Parigini, Ruben J. Sanchez-Garcia
Summary: The arrangement of cells in tissues forms a lineage hierarchy to regulate tissue turnover. Based on the relationship between cell molecular 'states' and cell 'types', a self-renewing cell type is shown to only reside at the top of the lineage hierarchy in dynamic equilibrium. The property of 'stemness' is entirely determined by the cell environment, supporting the idea that stem cell identities are contextual.
Article
Biochemistry & Molecular Biology
Daniel Taylor, Nia Verdon, Peter Lomax, Rosalind J. Allen, Simon Titmuss
Summary: In this study, a microfluidic device and imaging protocol were introduced for high-resolution imaging and automatic counting of bacteria within microdroplets. The researchers successfully tracked the stochastic growth of replicate Escherichia coli populations and found that the growth trajectories in early times followed the predictions of the Bellman-Harris model.
Article
Biochemical Research Methods
Ludovico Calabrese, Jacopo Grilli, Matteo M. Osella, Christopher Kempes, Marco Cosentino M. Lagomarsino, Luca Ciandrini, Jason M. Haugh, Oleg A. Igoshin
Summary: Cells adopt strategies to allocate resources under limited availability. Our study shows that at slow growth, protein degradation is balanced by maintenance ribosomes. We find that protein degradation increases at slow growth, possibly due to active waste management and recycling.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Physics, Multidisciplinary
Patrick Sinclair, Chris A. Brackley, Martin Carballo-Pacheco, Rosalind J. Allen
Summary: Surface-attached bacterial biofilms can lead to disease and industrial biofouling, and are widespread in natural environments. Quorum sensing is an important mechanism for biofilm initiation. We present and analyze a model that suggests a stochastic transition from loosely attached bacteria near the surface to a growing biofilm.
PHYSICAL REVIEW LETTERS
(2022)
Article
Cell Biology
Liam Barry-Carroll, Philip Greulich, Abigail R. Marshall, Kristoffer Riecken, Boris Fehse, Katharine E. Askew, Kaizhen Li, Olga Garaschuk, David A. Menassa, Diego Gomez-Nicola
Summary: Microglia are derived from the yolk sac and migrate into the brain during early embryonic development. They undergo in situ proliferation and ultimately colonize the entire brain by the third postnatal week in mice. This study reveals that their colonization is facilitated by clonal expansion of highly proliferative microglial progenitors distributed throughout the brain. Additionally, the spatial distribution of microglia changes from clustered to random during development.
Article
Biotechnology & Applied Microbiology
Ellen Young, Gavin Melaugh, Rosalind J. Allen
Summary: The emergence of spatial organisation in biofilm growth is investigated using individual-based simulations. It is found that the transition from smooth to rough interface morphologies is associated with dynamical changes in the active layer. The fluctuations in the active layer thickness play a central role in controlling the pinning of the biofilm interface and the resulting biofilm morphology.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Biotechnology & Applied Microbiology
Gavin Melaugh, Vincent A. Martinez, Perrin Baker, Preston J. Hill, P. Lynne Howell, Daniel J. Wozniak, Rosalind J. Allen
Summary: Researchers have found that Pseudomonas aeruginosa forms suspended multicellular aggregates in liquid media, and these aggregates may play important roles in disease and biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have been implicated in aggregation, but their roles vary depending on the growth stage of the bacterial cultures. Cell-associated Psl mediates aggregation in exponentially growing cultures, while both eDNA and Psl mediate cohesion in stationary phase cultures. These findings suggest that the properties of multicellular aggregates change throughout the growth cycle of P. aeruginosa.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Review
Cell & Tissue Engineering
Philip Greulich
Summary: This article gives an overview of quantitative modelling approaches in biology and provides guidance on how to use them in stem cell research. It points out that while quantitative modelling can boost biological research, careful considerations need to be taken to avoid pitfalls and understand its limitations.
CURRENT STEM CELL REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Pascal S. Rogalla, Timothy J. Rudge, Luca Ciandrini