Article
Engineering, Multidisciplinary
Tien Dung Le, Christian Moyne, Khaled Bourbatache, Olivier Millet
Summary: Macroscopic models for diffusion and heterogeneous reversible reaction of two species in porous media are developed using coupled homogenization technique and spectral approach. This approach is effective for upscaling diffusion-reaction microscopic problems, especially for high Damkohler number values, capturing the physics at very short times.
APPLIED MATHEMATICAL MODELLING
(2022)
Article
Mathematics
M. Gahn, I. S. Pop
Summary: In this work, a homogenization method is presented for a reaction-diffusion model with an evolving microstructure, which can be used to model mineral dissolution and precipitation in a porous medium. The model involves the evolution of the micro domain and the changing radii of spherical solid grains. By applying the Rothe-method, the existence of a weak solution is proved and a priori estimates that are uniform with respect to epsilon are obtained. Finally, a macroscopic model is derived by letting epsilon -> 0 using the method of two-scale convergence.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2023)
Article
Physics, Multidisciplinary
Joanna Janczura, Michal Balcerek, Krzysztof Burnecki, Adal Sabri, Matthias Weiss, Diego Krapf
Summary: The diffusion of nanoparticles in the cytoplasm of live cells shows a dichotomous switching between two distinct mobility states, with an overall subdiffusive mode of motion similar to fractional Brownian motion. The heterogeneity in experimental data is mainly due to variations in transport coefficients, rather than locally varying anomaly exponents. This approach demonstrates that diffusion heterogeneities can be accurately extracted and quantified from short trajectories obtained through single-particle tracking in complex media.
NEW JOURNAL OF PHYSICS
(2021)
Article
Water Resources
Tien Dung Le, Christian Moyne, Mohamed Khaled Bourbatache, Olivier Millet
Summary: A multi-species diffusion/heterogeneous reaction coupled problem in porous media involving a boundary layer problem is investigated. By utilizing a spectral approach, a macroscopic model is derived in the high Damkohler number regime, combining homogenization technique and spectral approach. However, this homogenized model cannot accurately represent the perturbation at the external boundary. To overcome this limitation, an improved model involving additional rapidly-decaying variables is proposed to capture the complex physics in the boundary layer. Numerical simulations validate the accuracy of the proposed correction method in both steady and transient states.
ADVANCES IN WATER RESOURCES
(2023)
Article
Engineering, Chemical
Mohamed Khaled Bourbatache, Tien Dung Le, Olivier Millet, Christian Moyne
Summary: This study focuses on upscaling of coupled diffusion-heterogeneous reaction problem in porous media for different orders of magnitude of the Damkohler number. It is found that the macroscopic model accurately predicts the coupled diffusion-reaction process at the macroscale in the range of small Damkohler number under slow reaction rate conditions, while errors occur under moderate and high reaction rates. Classical homogenization technique fails to capture the complex physics at short time when chemical equilibrium is not reached.
TRANSPORT IN POROUS MEDIA
(2021)
Article
Physics, Fluids & Plasmas
Diego M. Fieguth, Timo Schlachter, Daniel S. Brady, James R. Anglin
Summary: This study examines a Hamiltonian system representing an active particle that can move in noisy and dissipative environments by drawing energy from an internal depot. Despite energy dissipation to the environment, it can help stabilize the dynamic process of the active particle.
Article
Physics, Fluids & Plasmas
Stephy Jose, Dipanjan Mandal, Mustansir Barma, Kabir Ramola
Summary: This study investigates active lattice walks, biased continuous time random walks that undergo orientational diffusion between lattice directions in one and two spatial dimensions. The authors analyze the occupation probability, large deviation free-energy function, and moments and cumulants of displacements of an active particle in one and two dimensions. Exact results show persistent cross-correlations between motion in the x and y directions in two dimensions, and the large deviation function exhibits two regimes with different diffusive behaviors for active particles. Simulation results confirm the analytical findings.
Article
Chemistry, Physical
Julian Lee, Kyle Cotter, Ibrahim Elsadek, Matthew J. Comstock, Steve Presse
Summary: We investigated the hydrodynamic coupling between neighboring micro-beads in a dual optical trap system, which allowed us to control the coupling degree and measure the time-dependent trajectories of the entrained beads. Experimental results of a probe bead's average trajectory, entrained by the motion of a neighboring scan bead, were compared with theoretical computations, demonstrating the significance of viscous coupling and determining the relaxation timescales of the probe bead. These findings provide direct experimental evidence for hydrodynamic coupling at larger scales and longer timescales, which are relevant to hydrodynamic-assisted colloidal assembly and improving the resolution of optical tweezers. We conducted the experiments with three different bead setups.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Vincent Rossetto
Summary: This paper examines the solutions of the radiative transfer equation and their relationship with Green's functions, suggesting that the transitivity property can be achieved by considering the radiance distribution in phase space. Exact solutions are obtained in one and two dimensions using continuous-time persistent random walks, which correspond to the Fokker-Planck equation of the radiative transfer equation. The Lorentz covariance property is confirmed, and the measured signal from a pulse source in one dimension is discussed, unveiling an effective random delay when the pulse is emitted away from the observer.
Article
Automation & Control Systems
Yong Ren, Lanying Hu, Jiaying Li
Summary: This paper investigates the stability issues of stochastic reaction-diffusion systems driven by G-Brownian motion (G-SRDSs) in relation to a part of the variables. Using G-Lyapunov techniques and G-Ito's formula, the criteria of global practical uniform kth moment exponential stability and global practical uniform quasi surely exponential stability are established. An example is provided to demonstrate the usefulness and feasibility of the proposed results.
INTERNATIONAL JOURNAL OF CONTROL
(2023)
Article
Mathematics, Interdisciplinary Applications
Maike A. F. dos Santos, Luiz Menon Junior
Summary: This paper proposes two diffusion models for SBM with random diffusivity and shows the main features of each model through thorough analysis of simulation results. The first model is suitable for systems with consistently non-Gaussian diffusion, while the second model is suitable for systems with a transition from non-Gaussian to standard Gaussian processes.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Chemistry, Multidisciplinary
Yang Liu, Xu Zheng, Dongshi Guan, Xikai Jiang, Guoqing Hu
Summary: In this study, the impact of heterogeneous nanostructures on anomalous diffusion in dipalmitoylphosphatidylcholine (DPPC) monolayers is investigated. The existence of condensed nanodomains and their influence on diffusion are identified. The findings reveal a universal characteristic of multistage mean square displacement (MSD) and an anomalous double-peaked displacement probability distribution (DPD) phenomenon.
Article
Mathematics, Interdisciplinary Applications
M. A. F. dos Santos, E. H. Colombo, C. Anteneodo
Summary: This study focuses on the diffusion characteristics of fractional Brownian walkers, aiming to understand individual-level features through the temporal evolution of population spatial distribution. A general framework is developed to address the possibilities and limitations of connecting these features to various diffusion processes. The results are presented in terms of well-known processes, such as Laplace diffusion and nonlinear diffusion.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Physics, Fluids & Plasmas
Baruch Meerson
Summary: We evaluated the mean escape time of overdamped particles over potential barriers in short-correlated quenched Gaussian disorder potentials in one dimension at low temperature. The form of the tail of the potential barrier probability distribution has a significant impact on the thermally activated escape. We used the optimal fluctuation method to evaluate this tail. We found that for monotone decreasing autocovariances, the obtained tail is consistent with the result obtained by Lopatin and Vinokur (2001). However, for nonmonotonic autocovariances with negative autocorrelations, we observed a higher tail, leading to an exponential increase in the mean escape time. The transition between the two regimes exhibits characteristics of a first-order transition.
Article
Mechanics
F. Faisant, B. Besga, A. Petrosyan, S. Ciliberto, Satya N. Majumdar
Summary: This study experimentally investigates the optimal mean time for a Brownian particle to reach a target with resetting in one or two dimensions. Different resetting protocols were derived and tested, revealing a phase transition at a critical value, with calculations, experimental setup, and limitations discussed.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Cell Biology
Robert A. Marmion, Liu Yang, Yogesh Goyal, Granton A. Jindal, Joshua L. Wetzel, Mona Singh, Trudi Schupbach, Stanislav Y. Shvartsman
Summary: Terminal patterning in Drosophila embryos is regulated by ERK signaling, with recent studies focusing on gain-of-function variants of human MEK1, revealing both signal-independent kinase activity and signal-dependent activation mechanisms.
MOLECULAR BIOLOGY OF THE CELL
(2021)
Article
Cell Biology
Caroline A. Doherty, Rocky Diegmiller, Manisha Kapasiawala, Elizabeth R. Gavis, Stanislav Y. Shvartsman
Summary: A bidirectional communication mechanism between oocytes and nurse cells regulates the growth of germline cysts, with Dacapo playing a critical role in this process. This communication establishes a feedback mechanism that regulates the quantity of maternal resources loaded into the oocyte.
DEVELOPMENTAL CELL
(2021)
Article
Biophysics
Binglun Shao, Rocky Diegmiller, Stanislav Y. Shvartsman
Summary: The question of how network dynamics depend on network structure has been explored in the context of Drosophila oogenesis, where stable cytoplasmic bridges connect the future oocyte to nurse cells. Coordination of endoreplication cycles between the oocyte and nurse cells is influenced by retrograde transport of a cell cycle inhibitor, with intercellular connectivity within the oocyte-nurse cell cluster playing a role in collective dynamics.
BIOPHYSICAL JOURNAL
(2021)
Review
Cell Biology
Caroline A. Doherty, Farners Amargant, Stanislav Y. Shvartsman, Francesca E. Duncan, Elizabeth R. Gavis
Summary: This article discusses the bidirectional communication between oocytes and support cells, suggesting that it is a universal phenomenon that can be compared across species. By comparing the oogenesis in fruit flies and mice, this study highlights the similarities and differences between these systems, which can inform and design future experiments.
TRENDS IN CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tomer Stern, Stanislav Y. Shvartsman, Eric F. Wieschaus
Summary: Gastrulation movements in animal embryos are driven by regulated deformations of patterned epithelial sheets, and understanding the cellular processes and large-scale tissue deformations involved is crucial for studying animal development. Recent advances in microscopy and image processing provide a unique opportunity to integrate these complementary viewpoints, allowing for a better understanding of the early stages of gastrulation. By utilizing a computational framework for cell segmentation and tracking, as well as efficient algorithms for event detection, this study provides insights into the cellular activity patterns and quantitative relations between intercalation frequency and axis elongation during early Drosophila embryo gastrulation.
Article
Multidisciplinary Sciences
Claire J. Weaver, Aleena L. Patel, Stanislav Y. Shvartsman, Michael S. Levine, Nicholas Treen
Summary: This study investigates the regulation of transcription factor condensates by ERK signaling in embryos of a simple proto-vertebrate. The authors demonstrate that ERK signaling induces changes in the localization of transcriptional repressor ERF and observe dynamic assembly and dissociation of condensates during interphase. These findings provide insights into the regulation of gene activity and cell signaling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Shannon E. Keenan, Maria Avdeeva, Liu Yang, Daniel S. Alber, Eric F. Wieschaus, Stanislav Y. Shvartsman
Summary: In this study, gene editing and microscopy were used to investigate the gene regulatory network involved in fruit fly embryonic development. A computational approach was developed to merge image data of individual components into a multivariable trajectory. The research revealed a low intrinsic dimensionality of posterior patterning and cell fate determination, allowing the construction of a model and predictions at the protein level.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biophysics
Jaspreet Singh, Jasmin Imran Alsous, Krishna Garikipati, Stanislav Y. Shvartsman
Summary: This article investigates the assembly process of intercellular bridges (ICBs) during cytokinesis, analyzing the mechanical properties of ICBs and the interplay between ring contraction and stiffening through experimental and theoretical models. The results reveal a dynamic competition between contractility and stiffening, with overlapping time intervals necessary for proper assembly of ICBs.
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Robert A. Marmion, Alison G. Simpkins, Lena A. Barrett, David W. Denberg, Susan Zusman, Jodi Schottenfeld-Roames, Trudi Schupbach, Stanislav Y. Shvartsman
Summary: Germline mutations upregulating RAS signaling are associated with diverse developmental disorders. Utilizing controlled studies in Drosophila, researchers have discovered that activating variants of MEK, a core enzyme in the RAS pathway, cause phenotypic variations due to stochastic signaling variation. By quantifying cell fate specification errors, the study sheds light on the heterogeneity of developmental disorders caused by deregulated RAS signaling and provides a framework for investigating the effects of other pathogenic alleles and mild mutations.
Article
Chemistry, Multidisciplinary
Keonyong Lee, Kate Molloy O'Neill, Jayoung Ku, Stanislav Yefimovic Shvartsman, Yoosik Kim
Summary: The segmentation of the Drosophila embryo is regulated by localized maternal signals, including Bicoid and Nanos. The terminal system, controlled by mitogen-activated protein kinase, patterns the non-segmented termini. However, the spatial extent of this system in regulating gap genes beyond poles is unknown. Through study on mutagenized embryos, researchers discovered that the terminal system can establish multiple gene expression boundaries along the anteroposterior axis, displaying a potential bistability.
KOREAN JOURNAL OF CHEMICAL ENGINEERING
(2023)
Article
Biochemical Research Methods
Rocky Diegmiller, Jasmin Imran Alsous, Duojia Li, Yukiko M. Yamashita, Stanislav Y. Shvartsman
Summary: This study uses Drosophila melanogaster as a model to investigate the development of the shared organelle fusome in both male and female germline cysts. The findings reveal differences in the role and structure of the fusome between males and females, providing insights into the divergent outcomes of gametogenesis in different sexes. The study highlights the importance of quantitative measurements in biological sciences.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Pearson W. Miller, Daniel Fortunato, Cyrill Muratov, Leslie Greengard, Stanislav Shvartsman
Summary: This study investigates how altering the symmetry of a model impacts the dynamics of cell polarization. Through numerical and analytical techniques, non-trivial solutions for symmetry breaking are discovered.
NATURE COMPUTATIONAL SCIENCE
(2022)
Correction
Computer Science, Interdisciplinary Applications
Pearson W. Miller, Daniel Fortunato, Cyrill Muratov, Leslie Greengard, Stanislav Shvartsman
NATURE COMPUTATIONAL SCIENCE
(2022)
Review
Biology
Rocky Diegmiller, Hayden Nunley, Stanislav Y. Shvartsman, Jasmin Imran Alsous
Summary: This study presents mathematical models based on the dynamics of cell cycle proteins to explain the generation of germline cell lineage trees (CLTs) and highlights the diversity of observed CLT sizes and topologies across species. The study analyzes competing models of symmetry breaking in CLTs to rationalize the observed dynamics and robustness of oocyte fate specification, and explores how CLT topology affects cell cycle dynamics and synchronization.
Meeting Abstract
Biophysics
Keshav Patil, Stanislav Shvartsman, Ravi Radhakrishnan
BIOPHYSICAL JOURNAL
(2022)