Article
Physics, Fluids & Plasmas
A. Plati, A. Puglisi, A. Sarracino
Summary: We propose a thermodynamic uncertainty relation that constrains the average squared displacement of a Gaussian process with memory under the influence of unbalanced thermal baths and/or external forces. Our bound is more rigorous than previous results and is applicable at finite times. We verify our findings using experimental and numerical data from a vibrofluidized granular medium, which exhibits anomalous diffusion behavior. Our relation has the ability to discern between equilibrium and nonequilibrium dynamics in certain cases, which is challenging for Gaussian processes.
Article
Physics, Fluids & Plasmas
Cillian Cockrell, Ian J. Ford
Summary: The developing field of stochastic thermodynamics extends macroscopic thermodynamic concepts to the microscopic level. This framework is extended to consider non-Markovian environments, which exhibit a rich variety of behavior and affect entropy production.
Article
Multidisciplinary Sciences
Yusi Chen, Burke Q. Rosen, Terrence J. Sejnowski
Summary: Investigating neural interactions is crucial for understanding behavior, but accurately estimating the direction of network interactions remains challenging. This study introduces DDC, a method based on dynamical network models, which can detect directional interactions accurately under nonstationary conditions. DDC has good scalability and can be applied to various dynamical models and recording techniques.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Neurosciences
Jennifer Rollo, John Crawford, John Hardy
Summary: Alzheimer's disease is a complex pathology that requires non-linear dynamical systems modeling and community-wide participation to understand and predict its dynamics. A new methodology is proposed to integrate intuition and test system-level hypotheses and interventions.
Review
Physics, Multidisciplinary
Miguel A. S. Pinto, Tiberiu Harko, Francisco S. N. Lobo
Summary: In this work, the author explores the irreversibility thermodynamics of open systems and the potential of gravitationally generated particle production in modified gravity. Specifically, the author examines the scalar-tensor representation of f(R, T) gravity in which the non-conservation of the energy-momentum tensor leads to particle creation. The author derives and discusses the expressions for the particle creation rate, creation pressure, and entropy and temperature evolutions, and shows how these concepts can be applied to cosmological models.
Article
Engineering, Chemical
Hector Ramirez, Yann Le Gorrec, Bernhard Maschke
Summary: Boundary controlled irreversible port-Hamiltonian systems (BC-IPHS) are defined on a 1-dimensional spatial domain, characterized by the coupling between energy storing and energy dissipating elements. By extending the definition of boundary port variables, BC-IPHS can be passive with respect to a given set of conjugated inputs and outputs, while satisfying the first and second laws of Thermodynamics as a structural property of the system.
CHEMICAL ENGINEERING SCIENCE
(2022)
Article
Physics, Fluids & Plasmas
Diego Frezzato
Summary: When a fluctuating system is influenced by a time-dependent drive or nonconservative forces, the symmetry of its dynamics can be broken, resulting in an average bias. This study explores the imbalance between direct and inverse dynamical outputs, referred to as events, in a bidirectional forward-backward setup based on the fluctuation theorem. The probabilities of direct and inverse events occurring in both forward and backward modes are examined for systems in contact with a thermal bath. The findings include specialized results applicable to finite-time processes and systems in steady conditions, such as generalized thermodynamic uncertainty relations and constraints on the work distribution function.
Article
Mechanics
Lennart Dabelow, Stefano Bo, Ralf Eichhorn
Summary: The defining feature of active particles is their constant self-propulsion through the conversion of chemical energy into directed motion, keeping them permanently out of equilibrium. Despite potentially sharing certain equilibrium features, active particles may break the time-reversal symmetry in anharmonic potentials while fulfilling it in harmonic potentials in steady-state trajectories.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Physics, Multidisciplinary
Hector Ramirez, Yann Le Gorrec
Summary: This paper provides a comprehensive overview of the formulation of irreversible port-Hamiltonian systems for finite and infinite dimensional systems defined on 1D spatial domains in a unified manner. The formulation extends the classical port-Hamiltonian system formulation to handle irreversible thermodynamic systems. The formalism includes coupled thermo-mechanical systems and purely reversible or conservative systems.
Article
Computer Science, Interdisciplinary Applications
Meng Zhao, Lijian Jiang
Summary: In this paper, a data-driven non-parametric approach based on stochastic Koopman operator and extended dynamic mode decomposition (EDMD) is presented for forecasting the probability density evolution of stochastic dynamical systems. The approach uses EDMD to approximate the finite-dimensional eigendecomposition of the stochastic Koopman operator and leverages the connection between the generator and Fokker-Planck operator to construct an orthonormal basis for spectral decomposition of the probability density function. This method is capable of producing more accurate probability density forecasts than diffusion forecasting.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Mengnan Li, Lijian Jiang
Summary: In this article, the authors introduce data-driven reduced-order modeling for nonautonomous dynamical systems in multiscale media. They explain the use of the Koopman operator and its dependence on time pair in nonautonomous systems. To estimate time-dependent Koopman operators, a moving time window is used for data decomposition and the extended dynamic mode decomposition method is used. The authors propose reduced-order modeling as a strategy to solve the challenge of high-dimensional data and introduce offline and online stages. They also develop three methods for online reduced-order modeling: fully online, semi-online, and adaptive online. Numerical examples are provided to demonstrate the performance of different methods.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Automation & Control Systems
Manuel Lanchares, Wassim M. Haddad
Summary: Dissipative dynamical systems provide connections between physics, dynamical systems theory, and control science and engineering. Dissipativity theory has been extensively developed in the literature for the analysis and design of control systems based on generalized system energy considerations. Recently, there have been efforts to extend dissipativity notions to stochastic dynamical systems.
SYSTEMS & CONTROL LETTERS
(2023)
Article
Engineering, Mechanical
Mariya Mamajiwala, Debasish Roy
Summary: The proposed method presents a new approach for developing flows of stochastic dynamical systems on a Riemannian manifold by applying concepts from energetics to guide the flow. It is also applicable to simulations of Brownian dynamics and non-convex optimization problems.
PROBABILISTIC ENGINEERING MECHANICS
(2022)
Article
Physics, Multidisciplinary
Alberto Rolandi, Marti Perarnau-Llobet, Harry J. D. Miller
Summary: To achieve efficient and reliable control of microscopic systems, it is important to find driving protocols that minimize both average dissipation and stochastic fluctuations in work. In rapidly driven classical and quantum systems, we have characterized these optimal protocols, showing that they involve two discontinuous jumps in the full set of control variables. These jumps can be adjusted to interpolate between processes with minimal dissipation or minimal fluctuations, and sometimes allow for simultaneous minimization. We have demonstrated our general results using rapidly driven closed quantum systems, classical bit erasure, and a dissipative Ising chain driven close to a quantum phase transition.
NEW JOURNAL OF PHYSICS
(2023)
Article
Physics, Multidisciplinary
Bohdan Slavko, Mikhail Prokopenko, Kirill S. Glavatskiy
Summary: The study proposes a non-equilibrium framework for modeling the evolution of cities, describing intra-urban migration as an irreversible diffusive process and validating it with actual migration data from Australian capital cities. The population is shown to consist of two distinct groups with different relocation frequencies in terms of residential relocation. These groups can be interpreted as two components of a binary fluid mixture in the developed framework, each with its own diffusive relaxation time. The approach allows for long-term predictions of cities' spatial structures, defining their equilibrium population distribution.
Article
Multidisciplinary Sciences
David Orozco-Gomez, Juan Eduardo Sosa-Hernandez, Oscar Adrian Gallardo-Navarro, Jesus Santana-Solano, Moises Santillan
SCIENTIFIC REPORTS
(2019)
Editorial Material
Physics, Multidisciplinary
Luis Diambra, Moises Santillan
FRONTIERS IN PHYSICS
(2019)
Article
Biology
Aaron Vazquez-Jimenez, Moises Santillan, Jesus Rodriguez-Gonzalez
JOURNAL OF BIOLOGICAL SYSTEMS
(2019)
Article
Microbiology
Oscar Adrian Gallardo-Navarro, Moises Santillan
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Biology
Laura Sanchez-Gomez, Agustin Guerrero-Hernandez, Moises Santillan
JOURNAL OF THEORETICAL BIOLOGY
(2019)
Article
Biology
Jose G. Guerrero-Morin, Moises Santillan
JOURNAL OF THEORETICAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Jorge A. Arias-del-Angel, Jesus Santana-Solano, Moises Santillan, Rebeca G. Manning-Cela
SCIENTIFIC REPORTS
(2020)
Article
Microbiology
Jorge A. Arias-del-Angel, Rebeca G. Manning-Cela, Moises Santillan
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Mathematics, Applied
Jesus Pantoja-Hernandez, cF Brena-Medina, Moises Santillan
Summary: The clock and wavefront paradigm and Meinhardt-PORD model are two widely accepted models to explain somitogenesis. Recently, a hybrid model combining PORD and a wavefront gradient has been proposed to address the limitations of the original models. This new model offers a more comprehensive explanation for the embryonic process.
Editorial Material
Mathematics, Applied
Marc R. Roussel, Moises Santillan
Article
Biochemistry & Molecular Biology
Humberto Reyes-Pardo, Daniel P. Sanchez-Herrera, Moises Santillan
Summary: Diabetic neuropathy is a complication of diabetes caused by cellular damage from persistent hyperglycemia. This study investigates the impact of plasma membrane alterations on sensory neurons and sensitivity changes in a murine model for type-1 diabetes, suggesting a correlation between plasma membrane fluidity and mechanical stimuli-induced changes in cell calcium transients.
Article
Biochemistry & Molecular Biology
Julian Gonzalez-Ayala, Antonio Calvo-Hernandez, Moises Santilan
Summary: This study presents a chemical kinetics model for molecular energy converters based on previous research. The model views all molecular energy converters as linked enzymatic reactions, with one reaction running downhill the chemical potential gradient and driving the other uphill. The researchers investigate how enzyme reactions can be forced to go backwards using a basic kinetic model, and propose a thermodynamically consistent method of linking two enzymatic reactions. The resulting model is thoroughly investigated in the context of energy converters, and compared to experimental data.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Diego Andres Castro-Lopez, Luis E. Gonzalez de la Vara, Moises Santillan, Agustino Martinez-Antonio
Summary: This study proposes a new biotechnological working model for tryptophan production, which incorporates the activity of tryptophan secretion systems and genetic modifications made in two E. coli strains. The resulting deterministic model is able to simulate the tryptophan production levels achieved by genetically engineered E. coli strains in experiments.
FERMENTATION-BASEL
(2022)
Article
Mathematics, Applied
Jesus Pantoja-Hernandez, Moises Santillan
Summary: Somitogenesis is the process of segmenting presomitic mesoderm into somites along the anterior-posterior axis, driven by a genetic oscillator known as the segmentation clock. Proper synchronization of the segmentation clock among PSM cells is essential for normal somitogenesis, and factors like network size, cell interactions, and variability among cells can affect synchronization. Very small networks may not synchronize, while moderate variability and network connectivity can improve synchronization in large networks.
Article
Engineering, Mechanical
O. Diaz-Hernandez, Elizeth Ramirez-Alvarez, A. Flores-Rosas, C. I. Enriquez-Flores, M. Santillan, Pablo Padilla-Longoria, Gerardo J. Escalera Santos
JOURNAL OF COMPUTATIONAL AND NONLINEAR DYNAMICS
(2019)