Related papers: Emergence of information transmission in a prebiot…
We study a process of pattern formation for a generic model of species anchored to the nodes of a network where local reactions take place, and that experience non-reciprocal long-range interactions, encoded by the network directed links.…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
Biological systems are homochiral, raising the question of how a racemic mixture of prebiotically synthesized biomolecules could attain a homochiral state at the network level. Based on our recent results, we aim to address a related…
Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here I develop a framework for heredity and development that includes the cycling regulators…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
A common feature of biological self-organization is how active agents communicate with each other or their environment via chemical signaling. Such communications, mediated by self-generated chemical gradients, have consequences for both…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Reaction-diffusion-advection media on semi-infinite domains are important in chemical, biological and ecological applications, yet remain a challenge for pattern formation theory. To demonstrate the rich emergence of nonlinear traveling…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
The process of polymer condensation, i.e. the formation of bonds between reactive end-groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing polymer condensation in competition with cyclisation. Using a…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
The temporal analysis of products reactor provides a vast amount of transient kinetic information that may be used to describe a variety of chemical features including the residence time distribution, kinetic coefficients, number of active…
We consider a model for random deposition of monomers on a line with extrinsic precursor states. As the adsorbate coverage increases, the system develops non-trivial correlations due to the diffusion mediated deposition mechanism. In a…
A novel hierarchical model of complex network is proposed, and information propagation process taking place on top of the network is investigated. Our model is demonstrated to have small world property. We found that the frequency…
Stochastic reaction-diffusion processes may be presented in terms of integrable quantum chains and can be used to describe various biological and chemical systems. Exploiting the integrability of the models one finds in some cases good…
We investigate the behaviour of randomly cross-linked (co)polymer blends using a combination of replica theory and large-scale molecular dynamics simulations. In particular, we derive the analogue of the random phase approximation for…
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system called replicator equations, are a possible mechanism for…
The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events -- choices of gene templates, base pair…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…