29 papers · ranked by Valyu relevance
Yingru Liu, Yucheng Xing, Xuewen Yang, Xin Wang + 3 more
'Zhaoyue Chen'] Learning continuous-time stochastic dynamics is a fundamental and essential problem in modeling sporadic time series, whose observations are irregular and sparse in both time and dimension. For a given system whose latent states and observed data are multivariate, it is generally impossible to derive a…
Samuel J. Abplanalp, Eric A. Reavis, Thanh P. Le, Michael F. Green
Ecological momentary assessment (EMA) is a frequently used approach among clinical researchers to collect naturalistic data in real time. EMA data can provide insights into the temporal dynamics of psychological processes. Traditional methods used to analyze EMA data, such as hierarchical linear modeling and multilevel…
Peter G. Fennell, Sergey Melnik, James P. Gleeson
Continuous-time Markov process models of contagions are widely studied, not least because of their utility in predicting the evolution of real-world contagions and in formulating control measures. It is often the case, however, that discrete-time approaches are employed to analyze such models or to simulate them…
Shuyun Jiao, David Waxman
There are many instances, in subjects such as biology, where a population number, or related quantity, changes in discrete time. For the population number at time n = 0, 1, 2, . . ., written xn, we show that some exactly soluble cases of xn can be related to a different problem, where the number of individuals changes…
Enzo Acerbi, Teresa Zelante, Vipin Narang, Fabio Stella
Background Dynamic aspects of gene regulatory networks are typically investigated by measuring system variables at multiple time points. Current state-of-the-art computational approaches for reconstructing gene networks directly build on such data, making a strong assumption that the system evolves in a synchronous…
Farhan Khodaee, Rohola Zandie, Yufan Xia, Elazer R. Edelman
We propose a new theory for aging based on dynamical systems and provide a data-driven computational method to quantify the changes at the cellular level. We use ergodic theory to decompose the dynamics of changes during aging and show that aging is fundamentally a dissipative process within biological systems, akin to…
Ignacio S. Gomez, Bruno G. da Costa, Maike A. F. dos Santos
In this work we show how the concept of majorization in continuous distributions can be employed to characterize mixing, diffusive, and quantum dynamics along with the H-Boltzmann theorem. The key point lies in that the definition of majorization allows choosing a wide range of convex functions $ϕ$ for studying a given…
Yevhen F. Suprunenko, Aneta Stefanovska
Chronotaxic systems represent deterministic nonautonomous oscillatory systems which are capable of resisting continuous external perturbations while having a complex time-dependent dynamics. Until their recent introduction in Phys. Rev. Lett. 111, 024101 (2013) chronotaxic systems had often been treated as stochastic…
Henning Kirchberg, Abraham Nitzan, Hong Qian
We considered discrete and continuous representations of a thermodynamic process in which a random walker (e.g., a molecular motor on a molecular track) uses periodically pumped energy (work) to pass N sites and move energetically downhill while dissipating heat. Interestingly, we found that, starting from a discrete…
Roel Dobbe, Claire J. Tomlin
The advent of biological data of increasingly higher resolution in space and time has triggered the use of dynamic models to explain and predict the evolution of biological systems over space and time. Computer-aided system modeling and analysis in biology has led to many new discoveries and explanations that would…
Axel Schild
The local conservation of a physical quantity whose distribution changes with time is mathematically described by the continuity equation. The corresponding time parameter, however, is defined with respect to an idealized classical clock. We consider what happens when this classical time is replaced by a…
Sharma Yamijala, M. Belen Oviedo, Bryan Wong
This review focuses on the application of Density Functional Tight Binding (DFTB) to electronic-excited states, which has attracted significant attention for extending the computationally efficient approach to the time domain. The chapter highlights the use of real-time time-dependent-DFTB to probe the electron…
Authors not listed
Strong coupling and environmental memory render many open quantum systems intractable to classical computation. To overcome this barrier, we present a variational quantum algorithm capable of solving generalized form time-local quantum master equations directly on Noisy Intermediate-Scale Quantum (NISQ) processors. Our…
Roland Riek
The second law of thermodynamics, with its positive change of entropy for a system not in equilibrium, defines an arrow of time. Interestingly, also, causality, which is the connection between a cause and an effect, requests a direction of time by definition. It is noted that no other standard physical theories show…
Ching-Hao Wang, Sakib Matin, Ashish B. George, Kirill S. Korolev
Traveling fronts describe the transition between two alternative states in a great number of physical and biological systems. Examples include the spread of beneficial mutations, chemical reactions, and the invasions by foreign species. In homogeneous environments, the alternative states are separated by a smooth front…
Jane Kondev, Marc Kirschner, Hernan G. Garcia, Gabriel L. Salmon + 1 more
Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose, structure or function is achieved. A classic example is the way in which…
Miguel A. Durán-Olivencia
Background Models of evolutionary dynamics have long been dominated by a paradigm of gradualism, yet the fossil record consistently points to a history defined by punctuation. This disconnect between theory and data has left major macroevolutionary events, such as punctuated equilibria, explosive radiations, and mass…
Roland Riek, Atanu Chatterjee, Cyril Branciard
Causality describes the process and consequences from an action: a cause has an effect. Causality is preserved in classical physics as well as in special and general theories of relativity. Surprisingly, causality as a relationship between the cause and its effect is in neither of these theories considered a law or a…
Duncan Bossion, Sutirtha Chowdhury, Pengfei Huo
We present the rigorous theoretical framework of the generalized spin mapping representation for non- adiabatic dynamics. This formalism is based on the generators of the su(N) Lie algebra to represent N discrete electronic states, thus preserving the size of the original Hilbert space in the state representation. The…
Hosein Nasrolahpour
Almost all phenomena and structures in nature exhibit some degrees of fractionality or fractality. Fractional calculus and fractal theory are two interrelated concepts. In this article we study the memory effects in nature and particularly in biological structures. Based on this fact that natural way to incorporate…
Karnamohit Ranka, Christine M. Isborn
Real-time (RT) electron density propagation with time-dependent density functional theory (TDDFT) or Hartree-Fock (TDHF) is one of the most popular methods to model the charge transfer in molecules and materials. However, both RT-TDHF and RT-TDDFT within the adiabatic approximation are known to produce inaccurate…
Karnamohit Ranka, Christine M. Isborn
Real-time (RT) electron density propagation with time-dependent density functional theory (TDDFT) or Hartree-Fock (TDHF) is one of the most popular methods to model the charge transfer in molecules and materials. However, both RT-TDHF and RT-TDDFT within the adiabatic approximation are known to produce inaccurate…
N. Boulanger, F. Buisseret, V. Dehouck, F. Dierick + 1 more
Natural human movements are stereotyped. They minimise cost functions that include energy, a natural candidate from mechanical and physiological points of view. In time-changing environments, however, motor strategies are modified since energy is no longer conserved. Adiabatic invariants are relevant observables in…
Alan Hastings, Karen C. Abbott, Kim Cuddington, Tessa Francis + 4 more
There is a growing recognition that ecological systems can spend extended periods of time far away from an asymptotic state, and that ecological understanding will therefore require a deeper appreciation for how long ecological transients arise. Recent work has defined classes of deterministic mechanisms that can lead…
Gianmarco Ducci, Gennaro Vitucci, Philippe Chatelain, Renaud Ronsse
Migratory birds travel over impressively long distances. Consequently, they have to adopt flight regimes being both efficient - in order to spare their metabolic resources - and robust to perturbations. This paper investigates the relationship between both aspects, i.e. mechanical performance and stability in flapping…
Sergej Pankratow
For many years, I have conducted a sort of scientific diary in which I put facts and results that I liked at the moment or found interesting and useful. My principal motivation was to learn how clever people construct beautiful mathematical models out of physical garbage - incongruent sets of data, apparently disjoined…
Justin Eilertsen, Wylie Stroberg, Santiago Schnell
The determination of a substrate or enzyme activity by coupling of one enzymatic reaction with another easily detectable (indicator) reaction is a common practice in the biochemical sciences. Usually, the kinetics of enzyme reactions is simplified with singular perturbation analysis to derive rate or time course…
Authors not listed
Machine olfaction—the artificial replication of the sense of smell—faces significant challenges due to the absence of large, standardized training datasets. Unlike vision, language, and audio models, which benefit from extensive corpora such as ImageNet, GLUE, and AudioSet, olfaction lacks scaled equivalents and…
Soheil Saghafi, Pejman Sanaei
Resonance and synchronized rhythm are important phenomena and can be either constructive or destructive in dynamical systems in the nature, specifically in biology. There are many examples showing that the human’s body organs must maintain their rhythm in order to function properly. For instance, in the brain…