Related papers: Structural Cellular Hash Chemistry
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…
Standard chemical evolution models based on long-term infall are affected by a number of problems, evidenced by the analysis of the most recent data. Among these: (1) models rely on the local metallicity distribution, assuming its shape is…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…
Learning classifier systems (LCSs) are evolutionary machine learning algorithms, flexible enough to be applied to reinforcement, supervised and unsupervised learning problems with good performance. Recently, self organizing classifiers were…
We have studied four complex organic molecules (COMs), methyl formate ($CH_3OCHO$), dimethyl ether ($CH_3OCH_3$), formamide ($NH_2CHO$), and ethyl cyanide ($C_2H_5CN$), towards a large sample of 39 high-mass star-forming regions…
The accurate simulation of interface-dominated solid mechanics problems on complex microstructures remains challenging, particularly when interface-fitted quadrilateral or hexahedral meshes are difficult to generate. We extend the shifted…
Achieving better exploitation and exploration capabilities (EEC) have always been an important yet challenging issue in the design of evolutionary optimization algorithm (EOA). The difficulties lie in obtaining a good balance in EEC, which…
We propose an extension of the Schr\"odinger equation for a quantum system interacting with environment. This equation describes dynamics of auxiliary wave-functions $\mathbf{m}$, from which the system density matrix can be reconstructed as…
We present our recently developed 3-dimensional chemodynamical code for galaxy evolution. This code follows the evolution of different galactic components like stars, dark matter and different components of the interstellar medium (ISM),…
The objective of this paper is to give a rigorous analysis of a stochastic spatial model of producer-consumer systems that has been recently introduced by Kang and the author to understand the role of space in ecological communities in…
A stochastic configuration interaction method based on evolutionary algorithm is designed as an affordable approximation to full configuration interaction (FCI). The algorithm comprises of initiation, propagation and termination steps,…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Cells generally change their internal state to adapt to an environmental change, and accordingly evolve in response to the new conditions. This process involves phenotypic changes that occur over several different time scales, ranging from…
Within the project Evolution of Chemistry in the envelope of HOt corinoS (ECHOS), we present a study of sulphur chemistry in the envelope of the Class 0 source B335 through observations in the spectral range 7, 3, and 2 mm. We have modelled…
Recent advances in microscopy and 3D reconstruction methods have allowed for characterization of cellular morphology in unprecedented detail, including the irregular geometries of intracellular subcompartments such as membrane-bound…
We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe networks of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
We show how the characteristics of the evolutionary algorithm influence the evolvability of candidate solutions, i.e. the propensity of evolving individuals to generate better solutions as a result of genetic variation. More specifically,…