23 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…
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…
Bruce S Martin, Gideon S Bradburd, Luke J Harmon, Marjorie G Weber + 1 more
'Hernán López-Fernández'] Title: Abstract Rates of phenotypic evolution vary markedly across the tree of life, from the accelerated evolution apparent in adaptive radiations to the remarkable evolutionary stasis exhibited by so-called “living fossils.” Such rate variation has important consequences for large-scale…
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.…
Sahani Pathiraja, Philipp Wacker
equations for quadratic fitness landscapes Authors: ['Sahani Pathiraja' 'Philipp Wacker'] The replicator-mutator equation is a model for populations of individuals carrying different traits, with a fitness function mediating their ability to replicate, and a stochastic model for mutation. We derive analytical solutions…
Dimpi Thakuria, Abhay Srivastav, Brij Mohan, Asmita Kumari + 1 more
'Arun Kumar Pati'] The quantum speed limit describes how quickly a quantum system can evolve in time from an initial state to a final state under a given dynamics. Here, we derive a generalised quantum speed limit (GQSL) for arbitrary time-continuous evolution using the geometrical approach of quantum mechanics. The…
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…
B. S. Martin, M. G. Weber
Fossilized organisms only represent a small fraction of Earth’s evolutionary history, motivating “ancestral state reconstruction” techniques for inferring unobserved phenotypes of evolving lineages based on measurements of their relatives. Stochastic character mapping has emerged as a particularly powerful approach in…
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…
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…
Per Östborn
time Authors: ['Per Östborn'] The treatment of time in relativity does not conform to that in quantum theory. To resolve the discrepancy, a formalization of time is introduced in an accompanying paper, starting from the assumption that the treatment of time in physics must agree with our cognition. The formalization…
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…
Hanna Kokko
Fisher's fundamental theorem states that natural selection improves mean fitness. Fitness, in turn, is often equated with population growth. This leads to an absurd prediction that life evolves to ever-faster growth rates, yet no one seriously claims generally slower population growth rates in the Triassic compared…
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…
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…
Chao Wang, Min-Lan Li, Rui-Wu Wang
Understanding of any biological evolutions, such as speciation, adaptation behavior and biodiversity pattern, is based on a fundamental concept of fitness, in which natural selection implies the improvement and progress of fitness in either direct/indirect benefit or genetic transmission to the next generation.…
Julian Z. Xue, Leonid Chindelevich, Frédéric Guichard
Many well-documented macro-evolutionary phenomena, such as increases in organization hierarchy, or sudden and episodic creation of new taxa, still challenge current evolutionary theories. Here we show a new mechanism that can explain them. We begin by showing how the order of mutations can alter evolutionary…
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…
Eden Tian Hwa Ng, Akira R. Kinjo
Plasticity-led evolution (PLE), where evolution is initiated by the environmental induction of novel adaptive phenotypes, which is followed by genetic accommodation, has been proposed to remedy the difficulties of mutation-led evolution (MLE) implied by the standard evolutionary theory, according to which evolution is…
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…
Authors not listed
Molecular dynamics (MD) and hybrid quantum–classical (QM/MM) methods provide powerful tools for simulating chemical and biological systems, yet their application to long-timescale, strongly coupled processes remains limited by non-integrability, chaotic sensitivity, and extreme time-scale separation. These limitations…