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The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic…
The measurement of chemical abundances in planetary nebulae in nearby galaxies is now relatively straightforward. The challenge is to use these chemical abundances to infer the chemical evolution of their host galaxies. At this point, our…
We are encouraged by the improving abundance measurements for quasar damped absorption line systems to start a new study of galaxy chemical evolution from high to low redshifts. Our goal is a simple, robust model based on a synthesis of our…
In this paper, we propose a method for density-based clustering in high-dimensional spaces that combines Locality-Sensitive Hashing (LSH) with the Quick Shift algorithm. The Quick Shift algorithm, known for its hierarchical clustering…
Gas-phase processes were long thought to be the key formation mechanisms for complex organic molecules in star-forming regions. However, recent experimental and theoretical evidence has cast doubt on the efficiency of such processes.…
In this paper, a novel computational technique for finite discrete approximation of continuous dynamical systems suitable for a significant class of biochemical dynamical systems is introduced. The method is parameterized in order to affect…
The Galaxy is in continuous elemental evolution. Since new elements produced by dying stars are delivered to the interstellar medium, the formation of new enerations of stars and planetary systems is influenced by this metal enrichment. We…
We studied the long-term dynamics of evolutionary Swarm Chemistry by extending the simulation length ten-fold compared to earlier work and by developing and using a new automated object harvesting method. Both macroscopic dynamics and…
Selection is central to biological evolution, yet there has been no general experimental framework for quantifying selection in chemical systems before life. Here we demonstrate that selection in a prebiological chemical system can be…
Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. Here we first identify the rate constant limits under which the concentrations of a given set of species will tend to…
This paper reports simulations allowing for stochastic accretion and mass loss within closed and open systems modeled using a previously developed multi-population, multi-zone (halo, thick disk, thin disk) treatment. The star formation rate…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
We develop a model to implement metal enrichment in a cosmological context based on the hydrodynamical AP3MSPH code described by Tissera, Lambas and Abadi (1997).The star formation model is based on the Schmidt law and has been modified in…
Since stellar populations enhance particular element abundances according to the yields and lifetimes of the stellar progenitors, the chemical evolution of galaxies serves as one of the key tools that allows the tracing of galaxy evolution.…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
It is shown how traditional development of theories of fluids based upon the concept of physical clustering can be adapted to an alternative local clustering definition. The alternative definition can preserve a detailed valence description…
Characterizing exoplanetary atmospheres via Bayesian retrievals requires assuming some chemistry model, such as thermochemical equilibrium or parameterized abundances. The higher-resolution data offered by upcoming telescopes enables more…
Biological systems exhibit marked molecular asymmetry, with proteins based predominantly on L-amino acids and nucleic acids and carbohydrates largely composed of D-sugars. Explanations for homochirality include asymmetric photochemistry,…
We consider an evolutionary PDE system coupling the Cahn-Hilliard equation with singular potential, mass source and transport effects, to a Brinkman-type relation for the macroscopic velocity field and to a further equation describing the…