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With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Traditional clustering methods are limited when dealing with huge and heterogeneous groups of gene expression data, which motivates the development of bi-clustering methods. Bi-clustering methods are used to mine bi-clusters whose subsets…
The operations drip and mate considered in (mem)brane computing resemble the operations cut and recombination well known from DNA computing. We here consider sets of vesicles with multisets of objects on their outside membrane interacting…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Membrane systems are a biologically-inspired computational model based on the structure of biological cells and the way chemicals interact and traverse their membranes. Although their dynamics are described by rules, encoding membrane…
The objective of the paper is to identify laws and mechanisms that allow the creation of more order from disorder using natural means i.e., without the help of conscious beings. While this is not possible for the collection of all dynamical…
Linear thresholding systems have been used as a model of neural activation and more recently proposed as a model of gene regulation. Here we exhibit linear thresholding systems whose dynamics produce surprisingly long cycles.
Realizable spin models are investigated in a two superconducting flux qubit system. It is shown that a specific adjustment of system parameters in the two flux qubit system makes it possible to realize an artificial two-spin system that…
We present a detailed kinetic model for the Polymerase Chain Reaction, and model the probability of replication in terms of the physical parameters of the problem. Applying the theory of branching processes, we show the existance of a new…
We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional…
We introduce program splicing, a programming methodology that aims to automate the commonly used workflow of copying, pasting, and modifying code available online. Here, the programmer starts by writing a "draft" that mixes unfinished code,…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
Nonlinear coupling between inter- and intra-element dynamics appears as a collective behaviour of elements. The elements in this paper denote symptoms such as a bacterium having an internal network of genes and proteins, a reactive droplet,…
Self-replicability is the unique attribute observed in all the living organisms and the question how the life was physically initiated could be equivalent to the question how self-replicating informative polymers were formed in the abiotic…
Smart systems are characterised by their ability to analyse measured data in live and to react to changes according to expert rules. Therefore, such systems exploit appropriate data models together with actions, triggered by domain-related…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…