Related papers: Strong cooperativity and inhibitory effects in DNA…
A recurrent loop consisting of a single neuron is considered which is influenced by a chemical excitatory delayed synaptic feedback. We show the response of the system is dependent to the duration of the activity of the synapse which is…
A behaviour of molecular cluster with Lennard-Jones potential of interactions as Hamiltonian system is studied by computer simulation (molecular dynamics method). It is shown that complex periodic oscillations of the cluster as a whole are…
Large multidimensionality of high-throughput datasets pertaining to cell signaling and gene regulation renders it difficult to extract mechanisms underlying the complex kinetics involving various biochemical compounds (e.g., proteins,…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…
We use the context of dryland vegetation to study a general problem of complex pattern forming systems - multiple pattern-forming instabilities that are driven by distinct mechanisms but share the same spectral properties. We find that the…
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Recently, it has been confirmed that long duplex DNA molecules with sizes larger than several tens of kilo-base pairs (kbp), exhibit a discrete conformational transition from an elongated coil state to a compact globule state upon the…
DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical…
A variety of phenomena connected with the formation of a dinuclear complex is observed in the heavy ion collisions at low energies. The dinuclear system model allows us to analyze the experimental data and to interpret them by comparison of…
Many networks are complex dynamical systems, where both attributes of nodes and topology of the network (link structure) can change with time. We propose a model of co-evolving networks where both node at- tributes and network structure…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
In recent experiments with ion traps, long-range interactions were associated with the exceptionally fast propagation of perturbation, while in some theoretical works they have also been related with the suppression of propagation. Here, we…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…
In this paper we consider piecewise affine differential equations modeling gene networks. We work with arbitrary decay rates, and under a local hypothesis expressed as an alignment condition of successive focal points. The interaction graph…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the…