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
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
Physics, Applied
Andrey G. Cherstvy, Hadiseh Safdari, Ralf Metzler
Summary: We investigated a diffusion process with a time-dependent diffusion coefficient and found different behaviors of particle displacement in both overdamped and underdamped limits. The results are applicable to a class of physical systems out of thermal equilibrium where rapid changes in diffusivity occur.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2021)
Article
Mathematics
Richard L. Magin, Ervin K. Lenzi
Summary: Fractional-order time and space derivatives enhance classical diffusion equations to explain non-Gaussian processes. Phase diagrams display different diffusion propagators (Gaussian, Cauchy), specific stochastic models (Levy process, subordinated Brownian motion), and regions of super- and sub-diffusion. Anomalous diffusion phase cubes classify models of anomalous diffusion using lines of super-diffusion, sub-diffusion, and quasi-Gaussian behavior.
Article
Chemistry, Physical
Francesco Piazza
Summary: The use of absorbing boundary conditions for diffusion-based problems in physical chemistry and biochemistry is common, but the explicit consideration of degradation and the geometry of reaction boundaries is often overlooked. In this study, a simple and general idea is introduced to derive appropriate boundary conditions based on the chemical reaction scheme and physical reaction boundaries. The results show that this mathematical analysis provides unique physical insight not accessible through standard treatments.
JOURNAL OF CHEMICAL PHYSICS
(2022)
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
Neurosciences
Christian Lee, Zheng Zhang, Skirmantas Janusonis
Summary: This study investigates whether there is a similar random dropout mechanism in biological neural networks as in artificial neural networks. The authors propose that serotonergic fibers in the brain may meet the criteria for a dropout-like mechanism due to their presence, stochastic structure, and growth throughout an individual's lifespan. By modeling the trajectories of serotonergic fibers, the study demonstrates the potential implementation of a dropout-like mechanism in brain tissue, supporting neuroplasticity. The results also suggest the use of mathematical theories of serotonergic fiber structure and dynamics in the design of dropout algorithms in artificial neural networks.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Physics, Multidisciplinary
Kanta Masuki, Hiroyuki Sudo, Masaki Oshikawa, Yuto Ashida
Summary: In this study, the researchers reveal new phenomena in dissipative quantum phase transitions in Josephson junctions through numerical and analytical renormalization group analyses, challenging conventional understandings and identifying the underlying mechanism.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Niladri Sekhar Mandal, Ayusman Sen, R. Dean Astumian
Summary: Single enzyme chemotaxis refers to the creation and maintenance of an enzyme's nonequilibrium spatial distribution through concentration gradients of the substrate and product. This phenomenon can occur naturally or experimentally. This paper proposes a mechanism based on diffusion and chemical reaction, demonstrating that kinetic and diffusion asymmetries determine the direction of chemotaxis. The results suggest that systems evolve to attain greater kinetic stability and accumulate in regions with smaller effective diffusion coefficients. Additionally, the presence of nonreciprocal attraction and repulsion between enzymes in a catalytic cascade is important in active matter behavior.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Polymer Science
Chao-ran Qin, Rui-jing Huang, Xiang-yan Song, Wen-de Tian
Summary: Inhibition of fibril assembly is a potential therapeutic strategy in neurodegenerative disorders. PAMAM dendrimers have shown promise in the treatment of Parkinson's disease but the mechanism of their interaction with NAC fragments is still unclear. This study used molecular dynamics simulation to investigate the interaction between PAMAM dendrimers and NAC fragments and found that PAMAM molecules can slow down the aggregation process and increase the formation time of the largest cluster.
ACTA POLYMERICA SINICA
(2023)
Article
Chemistry, Physical
Maria M. Reif, Martin Zacharias
Summary: This study presents an approach combining alchemical modifications and physical-pathway methods to calculate absolute binding free energies. It demonstrates the successful use of simultaneous alchemical transformations and physical ligand unbinding for potential of mean force calculations and nonequilibrium pulling simulations, as well as the benefits of reducing ligand-protein interactions prior to potential of mean force calculations. These methods show promise in reducing sampling problems and improving efficiency in protein-protein binding free energy calculations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Environmental Sciences
Yuqin Wang, Jiang Liu, Van Liem-Nguyen, Shanyi Tian, Siqi Zhang, Dingyong Wang, Tao Jiang
Summary: DOM influences the environmental fate and toxic effects of trace metals such as mercury. Different DOM isolates showed a wide range of binding strengths to Hg(II) due to their heterogeneous properties. DOM chromophores, including aromaticity and molecular weight, are critical indicators of the DOM-Hg affinity in ambient-relevant circumstances. Higher terrestrial DOM led to greater DOM-Hg affinity. UV-Vis and fluorescence spectroscopy can be used to estimate DOM composition and its binding strength with Hg(II). The relationship between logK and DOM properties provides a possible pathway of explanation for the spatial co-variations between Hg(II) concentrations and DOM characters observed in previous field investigations.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
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
Mechanics
Cecile Monthus
Summary: This study reformulates the research on the conditioning of Brownian motion and random walks on global dynamical constraints as a general framework for the 'microcanonical conditioning' of Markov processes on time-additive observables. It applies to various types of Markov processes and explores the link with the 'canonical conditioning' based on the generating function of the time-additive observable.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Multidisciplinary Sciences
Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, Yuji Sugita
Summary: The cell is crowded with proteins and other biomolecules, and the binding dynamics of an inhibitor with c-Src kinase can change in crowded environments compared to dilute solutions, potentially due to local conformational shifts in c-Src kinase. The presence of crowders like bovine serum albumins can reduce the efficacy of the inhibitor in experimental assays, highlighting the importance of understanding ligand binding pathways in crowded cellular environments.
NATURE COMMUNICATIONS
(2021)
Article
Neurosciences
Giuseppe Gangarossa, Sylvie Perez, Yulia Dembitskaya, Ilya Prokin, Hugues Berry, Laurent Venance
Editorial Material
Computer Science, Artificial Intelligence
Carole Knibbe, Guillaume Beslon, Dusan Misevic
Article
Computer Science, Artificial Intelligence
Sergio Peignier, Christophe Rigotti, Guillaume Beslon
COMPUTATIONAL INTELLIGENCE
(2020)
Article
Computer Science, Artificial Intelligence
Vincent Liard, David P. Parsons, Jonathan Rouzaud-Cornabas, Guillaume Beslon
Article
Mathematical & Computational Biology
Kerstin Lenk, Eero Satuvuori, Jules Lallouette, Antonio Ladron-de-Guevara, Hugues Berry, Jari A. K. Hyttinen
FRONTIERS IN COMPUTATIONAL NEUROSCIENCE
(2020)
Article
Computer Science, Artificial Intelligence
Joel Lehman, Jeff Clune, Dusan Misevic, Christoph Adami, Lee Altenberg, Julie Beaulieu, Peter J. Bentley, Samuel Bernard, Guillaume Beslon, David M. Bryson, Nick Cheney, Patryk Chrabaszcz, Antoine Cully, Stephane Doncieux, Fred C. Dyer, Kai Olav Ellefsen, Robert Feldt, Stephan Fischer, Stephanie Forrest, Antoine Frenoy, Christian Gagn, Leni Le Goff, Laura M. Grabowski, Babak Hodjat, Frank Hutter, Laurent Keller, Carole Knibbe, Peter Krcah, Richard E. Lenski, Hod Lipson, Robert MacCurdy, Carlos Maestre, Risto Miikkulainen, Sara Mitri, David E. Moriarty, Jean-Baptiste Mouret, Anh Nguyen, Charles Ofria, Marc Parizeau, David Parsons, Robert T. Pennock, William F. Punch, Thomas S. Ray, Marc Schoenauer, Eric Shulte, Karl Sims, Kenneth O. Stanley, Francois Taddei, Danesh Tarapore, Simon Thibault, Richard Watson, Westley Weimer, Jason Yosinski
Article
Physics, Multidisciplinary
Maxime Woringer, Ignacio Izeddin, Cyril Favard, Hugues Berry
FRONTIERS IN PHYSICS
(2020)
Article
Ecology
Charles Rocabert, Guillaume Beslon, Carole Knibbe, Samuel Bernard
Article
Mathematical & Computational Biology
Hugues Berry, Stephane Genet
Summary: Neurons in the deep cerebellar nuclei (DCNn) can switch between firing spikes and a stable depolarized state, with a new biophysical model explaining this behavior through the concept of limit cycles. The model suggests that current injections and blocking of calcium currents can induce these transitions. Additionally, simulations indicate that physiological synaptic inputs may trigger transitions between different states in the neurons.
JOURNAL OF MATHEMATICAL NEUROSCIENCE
(2021)
Article
Biochemical Research Methods
Lisa Blum Moyse, Hugues Berry
Summary: Up-Down synchronization in neuronal networks can be modulated by gliotransmission events from astrocytes, as demonstrated in our three-population neural network model.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Neurosciences
Audrey Denizot, Misa Arizono, U. Valentin Nagerl, Hugues Berry, Erik De Schutter
Summary: This study investigates the relationship between astrocytic nanoscale morphology and Ca2+ activity using computational tools and idealized 3D geometries. The results demonstrate that astrocytic morphology significantly influences Ca2+ signals, with swelling hindering signal propagation. This highlights the importance of astrocyte morphology in neuron-astrocyte communication, particularly in pathological conditions.
Article
Biochemical Research Methods
Leonardo Trujillo, Paul Banse, Guillaume Beslon
Summary: In this study, a minimal model of sequence inversions is introduced to simulate adaptive walks in molecular evolution. The results show that compared to point mutations, inversion mutations can allow the evolutionary process to escape local fitness peaks and reach higher fitness values.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yulia Dembitskaya, Charlotte Piette, Sylvie Perez, Hugues Berry, Pierre J. Magistretti, Laurent Venance
Summary: The study shows that glucose and lactate play different roles in memory engram and neural computation. Lactate is important for high-stimulation load activity patterns and high attentional load in cognitive tasks, while glucose is sufficient for less demanding neural computation and learning tasks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Computer Science, Information Systems
Remy Kusters, Dusan Misevic, Hugues Berry, Antoine Cully, Yann Le Cunff, Loic Dandoy, Natalia Diaz-Rodriguez, Marion Ficher, Jonathan Grizou, Alice Othmani, Themis Palpanas, Matthieu Komorowski, Patrick Loiseau, Clement Moulin Frier, Santino Nanini, Daniele Quercia, Michele Sebag, Francoise Soulie Fogelman, Sofiane Taleb, Liubov Tupikina, Vaibhav Sahu, Jill-Jenn Vie, Fatima Wehbi
FRONTIERS IN BIG DATA
(2020)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Quentin Carde, Marco Foley, Carole Knibbe, David P. Parsons, Jonathan Rouzaud-Cornabas, Guillaume Beslon
ALIFE 2019: THE 2019 CONFERENCE ON ARTIFICIAL LIFE
(2019)