PML nuclear bodies (NBs) are involved in the regulation of key pathways but their biochemical function metabolism is unknown. In this study NB assembly dynamics were assessed by live cell imaging and mathematic modeling its major component parts. We show that all six isoforms exhibit individual exchange rates at NBs identify V as a scaffold subunit. SP100 exchanges least five times faster than proteins. Turnover modulated SUMOylation. Exchange not temperature-dependent depletion cellular ATP...

Abstract Background We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation combinatorially complex chemical reaction systems. In our molecules possess location in reactor as well an orientation and geometry, while reactions are carried out according to list implicitly specified rules. Because rules can contain patterns molecules, or even infinitely sized network be defined. For implementation (based on LAMMPS), we have chosen already existing...

Two related but somewhat different approaches have been proposed to formalize the notion of a self-sustaining chemical reaction network. One is collectively autocatalytic sets, formalized as RAF theory, and other organization theory. Both formalisms argued be relevant origin life. sets organizations are defined differently, previously some relationships between two shown. Here, we refine explore these connections in more detail. In particular, show that so-called closed RAFs organizations,...

Abstract Many studies report age as a risk factor for BoHV-1 infection or seropositivity. However, it is unclear whether this pattern reflects true epidemiological causation consequence of study design and other issues. Here, we seek to understand the age-related dynamics seroprevalence in seasonal calving Irish dairy herds provide decision support implementation effective testing strategies. We analysed data from taken during two surveys conducted between 2010 2017. Age-dependent profiles...

Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity reflected by a reaction-diffusion medium. We illustrate ideas chemical considering Belousov-Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality demonstrated. For different methods coding constructions simplest signal devices described. function performed particular device determined geometrical...

Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State the art domain-specific algorithms combine quantization, Huffman encoding occasionally domain knowledge. We propose high resolution scheme (HRTC) that relies on piecewise linear functions to approximate quantized trajectories. By splitting error budget between quantization approximation, our approach beats current state by...

Cycles are abundant in most kinds of networks, especially biological ones. Here, we investigate their role the evolution a chemical reaction system from one self-sustaining composition molecular species to another and influence on stability these compositions. While it is accepted that, topological standpoint, they enhance network robustness, consequence cycles dynamics not well understood. In former study, developed necessary criterion for existence fixed point, which purely based...

In this paper, we present general methods that can be used to explore the information processing potential of a medium composed oscillating (self-exciting) droplets. Networks Belousov–Zhabotinsky (BZ) droplets seem especially interesting as chemical reaction-diffusion computers because their time evolution is qualitatively similar neural network activity. Moreover, such networks self-generated in microfluidic reactors. However, it hard track and understand function performed by due its...

Abstract Motivation: The functioning of many biological processes depends on the appearance only a small number single molecular species. Additionally, observation crowding leads to insight that even high copies species do not guarantee their interaction. How particles contribute stabilizing systems is well understood yet. Hence, we aim at determining influence molecules long-term behaviour systems, i.e. whether they can reach steady state. Results: We provide theoretical considerations and...

We examine the qualitative dynamics of a catalytic self-organizing system binary strings that is inspired by chemical information processing metaphor. A string interpreted in two different ways: either (a) as raw data or (b) machine able to process another order produce third one. This article focuses on phenomena evolution whose appearance notable because no explicit mutation, recombination, artificial selection operators are introduced. call self-evolving every variation performed objects...

A large training set of fitness cases can critically slow down genetic programming, if no appropriate subset selection method is applied. Such a allows an individual to be evaluated on smaller cases. In this paper we suggest new that takes the problem structure into account, while being independent at same time. order achieve this, information about acquired during evolutionary search by creating topology (relationship) The induced individuals evolving population. This done increasing...

Abstract Motivation: Novel techniques are required to analyze computational models of intracellular processes as they increase steadily in size and complexity. The theory chemical organizations has recently been introduced such a technique that links the topology biochemical reaction network their dynamical repertoire. is decomposed into algebraically closed self-maintaining subnetworks called organizations. They form hierarchy representing all feasible system states including steady states....

Abstract An integral equation is derived for a mean magnetic field in random velocity that renovates after characteristic time τ. It shown two cases, i.e. when (a) the correlation short, τ < l/v 0 (where l and v are scale velocity), (b) long wave components of field, k −1 ≫ τ, reduced to differential one, whose form has first been given by S TEENBECK , K RAUSE R ÄDLER . Expressions coefficients obtained above cases. In general case cannot be one although its spectral properties close...

The Mitotic Spindle Assembly Checkpoint ((M)SAC) is an evolutionary conserved mechanism that ensures the correct segregation of chromosomes by restraining cell cycle progression from entering anaphase until all have made proper bipolar attachments to mitotic spindle. Its malfunction can lead cancer.We constructed and validated for human (M)SAC in silico dynamical model, integrating 11 proteins complexes. model incorporates perspectives three central control pathways, namely Mad1/Mad2 induced...

Chemical organization theory has been suggested as a new approach to analyze complex reaction networks. Concerning the long-term behavior of network dynamics we will study its foundations mathematically. Therefore consider chemical reactor containing molecules different species reacting with each other according set rules. We further assume that dynamical concentration is given by continuous ordinary differential equation. Abstracting from dedicated values discrete problem: Which can appear...

A common problem in the analysis of biological systems is combinatorial explosion that emerges from complexity multi-protein assemblies. Conventional formalisms, like differential equations, Boolean networks and Bayesian networks, are unsuitable for dealing with explosion, because they designed a restricted state space fixed dimensionality. To overcome this problem, rule-based modeling language, BioNetGen, spatial extension, SRSim, have been developed. Here, we describe how to apply...

Recently, biochemical systems have been shown to possess interesting computational properties. In a parallel development, the chemical computation metaphor is becoming more and frequently used as part of emergent paradigm in computer science. We review this contribution idea behind outline its relevance for nanotechnology. set up simulated reaction system mathematical objects examine dynamics by experiments. Typical problems science, such sorting, parity checking or prime number are placed...

Abstract We consider the one‐dimensional weakly asymmetric nearest neighbour exclusion process and study, in macroscopic space‐time coordinates, fluctuations of associated density field around solution nonlinear BURGERS equation with viscosity. show that this converge to a generalized ORNSTEIN‐UHLENBECK process, drift term which can be obtained by linearization equation. Our approach is based on transformation process.