Related papers: Statistical mechanics of ecosystem assembly
We describe some of the important physical characteristics of the `pathways', i.e. dynamical processes, by which molecular, nanoscale and micron-scale self-assembly occurs. We highlight the fact that there exist features of self-assembly…
A fundamental problem in community ecology is to understand how ecological processes such as selection, drift, and immigration give rise to observed patterns in species composition and diversity. Here, we present a simple, analytically…
We propose dynamical systems trees (DSTs) as a flexible class of models for describing multiple processes that interact via a hierarchy of aggregating parent chains. DSTs extend Kalman filters, hidden Markov models and nonlinear dynamical…
We study a system of $N$ interacting particles on $\bf{Z}$. The stochastic dynamics consists of two components: a free motion of each particle (independent random walks) and a pair-wise interaction between particles. The interaction belongs…
The evolution of complex correlated quantum systems such as random circuit networks is governed by the dynamical buildup of both entanglement and entropy. We here introduce a real-time field theory approach -- essentially a fusion of the $G…
In any Markov chain with finite state space the distribution of transition records always belongs to the exponential family. This observation is used to prove a fluctuation theorem, and to show that the dynamical entropy of a stationary…
A one dimensional non-equilibrium stochastic model is proposed where each site of the lattice is occupied by a particle, which may be of type A or B. The time evolution of the model occurs through three processes: autocatalytic generation…
Diversity is a fundamental feature of ecosystems, even when the concept of ecosystem is extended to sociology or economics. Diversity can be intended as the count of different items, animals, or, more generally, interactions. There are two…
We propose a simple framework to understand commonly observed crisis waves in macroeconomic Agent Based models, that is also relevant to a variety of other physical or biological situations where synchronization occurs. We compute exactly…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
We consider a strictly substochastic matrix or an stochastic matrix with absorbing states. By using quasi-stationary distributions one shows there is a canonical associated stationary Markov chain. Based upon $2-$stringing representation of…
Autoregressive generative models -- including Transformers, recurrent neural networks, classical Kalman filters, state space models, and Mamba -- all generate sequences by sampling each output from a deterministic summary of the past,…
We propose a toy-model theory, that mimics various characteristic features of quantum mechanics. Unlike the toy-models previously studied in the literature, our toy-model allows for an observer to have a full knowledge of a system's real…
Populations experience a complex interplay of continuous and discrete processes: continuous growth and interactions are punctuated by discrete reproduction events, dispersal, and external disturbances. These dynamics can be modeled by…
In this paper, we study a special case of the invasion fitness matrix in a replicator equation: the invader-driven case. In this replicator, each species is defined by its unique active invasiveness potential (initial growth rate when…
We study the stochastic dynamics of a system of interacting species in a stochastic environment by means of a continuous-time Markov chain with transition rates depending on the state of the environment. Models of gene regulation in systems…
We develop exact simulation (also known as perfect sampling) algorithms for a family of assemble-to-order systems. Due to the finite capacity, and coupling in demands and replenishments, known solving techniques are inefficient for larger…
We show that the Tile Assembly Model exhibits a strong notion of universality where the goal is to give a single tile assembly system that simulates the behavior of any other tile assembly system. We give a tile assembly system that is…
The population dynamics and stability of ecosystems of interacting species is studied from the perspective of non-equilibrium thermodynamics by assuming that species, through their biotic and abiotic interactions, are units of entropy…
This paper develops a Bayesian mechanics for adaptive systems. Firstly, we model the interface between a system and its environment with a Markov blanket. This affords conditions under which states internal to the blanket encode information…