25 papers · ranked by Valyu relevance
Andrea Pagnani, Pierre Barrat-Charlaix
Protein evolution is fundamentally shaped by epistasis, where the effect of a mutation depends on the sequence context. As standard phylogenetic methods assume independently evolving sites, there is a need for more complex models based on accurate estimations of the fitness landscape. Good candidates are modern…
Andrea Pagnani, Pierre Barrat-Charlaix
Protein evolution is fundamentally shaped by epistasis, where the effect of a mutation depends on the sequence context. As standard phylogenetic methods assume independently evolving sites, there is a need for more complex models based on accurate estimations of the fitness landscape. Good candidates are modern…
Meike T. Wortel, Han Peters, Nils Chr. Stenseth
The Red Queen Hypothesis, which suggests that continual evolution can result from solely biotic interactions, has been studied in macroevolutionary and microevolutionary contexts. While the latter has been effective in describing examples in which evolution does not cease, describing which properties lead to continual…
Michael Doebeli, Yaroslav Ispolatov, Burt Simon, Wenying Shou
Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or…
Per Östborn
Relativistically, time t may be seen as an observable, just like position r. In quantum theory, t is a parameter, in contrast to the observable r. This discrepancy suggests that there exists a more elaborate formalization of time, which encapsulates both perspectives. Such a formalization is proposed in this paper. The…
Fernando Montaner, Irene Paniello
We formulate the notion of continuous evolution algebra in terms of differentiable matrix-valued functions, to then study those such algebras arising as solutions of ODE problems. Given their dependence on natural bases, matrix Lie groups provide a suitable framework where considering time-variant evolution algebras.…
Roland Riek
This is the version of the article before peer review or editing, as submitted by an author to insert name of Journal. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at doi =…
Arto Annila, Roland Riek
About a century ago, in the spirit of ancient atomism, the quantum of light was renamed the photon to suggest that it is the fundamental element of everything. Since the photon carries energy in its period of time, a flux of photons inexorably embodies a flow of time. Thus, time comprises periods as a trek comprises…
Arto Annila, Karo Michaelian
Evolution is customarily perceived as a biological process. However, when formulated in terms of physics, evolution is understood to entail everything. Based on the axiom of everything comprising quanta of actions (e.g., quanta of light), statistical physics describes any system evolving toward thermodynamic balance…
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…
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…
I. F. Ginzburg
The values of many phenomena in the Nature z are determined in some discrete set of times tn, separated by a small interval ∆t (which may also represent a coordinate, etc.). Let the z value in neighbour point tn+1 = tn + ∆t be expressed by the evolution equation as z(tn+1) ≡ z(tn +∆t) = f(z(tn)). This equation gives a…
Alyssa Adams, Hector Zenil, Paul C. W. Davies, Sara Imari Walker
Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems…
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…
Stephen De Lisle, Erik I. Svensson
Rates of molecular, phenotypic, and lineage diversification typically scale negatively with time interval of measurement, raising longstanding questions about time-dependency of evolutionary processes. These patterns and their potential meaning have recently re-entered evolutionary discussions. In this Perspective we…
Bengt Autzen, Samir Okasha
In a recent paper, Takacs and Bourrat (Biol Philos 37:12, 2022) examine the use of geometric mean reproductive output as a measure of biological fitness. We welcome Takacs and Bourrat’s scrutiny of a fitness definition that some philosophers have adopted uncritically. We also welcome Takacs and Bourrat’s attempt to…
Krzysztof Bartoszek
An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation…
Klara L. Verbyla, Von Bing Yap, Anuj Pahwa, Yunli Shao + 2 more
'Gavin A. Huttley' 'Konrad Scheffler'] Continuous-time Markov processes are often used to model the complex natural phenomenon of sequence evolution. To make the process of sequence evolution tractable, simplifying assumptions are often made about the sequence properties and the underlying process. The validity of one…
Nicolai Machholdt Høyer, Ove Christiansen
We present a new quasi-direct quantum molecular dynamics computational method which offer a compromise between quantum dynamics using a pre-computed potential energy surface (PES) and fully direct quantum dynamics. This method is termed the time-dependent adaptive density-guided approach (TD-ADGA) and is a method for…
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…
Eric Koessler, Arkajit Mandal, Pengfei Huo
We derive the L-MFE method to incorporate Lindblad jump operator dynamics into the mean-field Ehrenfest (MFE) approach. We map the density matrix evolution of Lindblad dynamics onto pure state coefficients using trajectory averages. We use simple assumptions to construct the L-MFE method that satisfies this exact…
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…
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…
Umberto Lucia, Giulia Grisolia
Causality is the relationship between causes and effects. Following Relativity, any cause of an event must always be in the past light cone of the event itself, but causes and effect must always be related to some interactions. In this paper, causality is developed as a consequence of the analysis of the Einstein…
Umberto Lucia, Giulia Grisolia
Causality is the relationship between causes and effects. Following Relativity, any cause of an event must always be in the past light cone of the event itself, but causes and effect must always be related to some interactions. In this paper, causality is developed as a consequence of the analysis of the Einstein…