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Bio Systems

S Eh Shirmovsky, D V Shulga
The paper investigates microtubules lattice properties taking into consideration elastic, dipole-dipole interaction of tubulins and viscosity. A microtubule is modeled as a system of bound tubulins, forming a skewed hexagonal two-dimensional lattice. Wave frequencies and group velocities have been calculated. Calculations have been performed for various directions of wave front propagation: helix, along the protofilament, and anti-helix. Three different wave polarization directions have been considered. It has been shown that the direction of the wave polarization influences the frequency and wave group velocity values in the lattice considerably...
March 8, 2018: Bio Systems
Sanjeev Kumar, Karmeshu
A theoretical investigation is presented that characterizes the emerging sub-threshold membrane potential and inter spike interval (ISI) distributions of an ensemble of IF neurons that group together and fire together. The noise intensity of the ensemble of neurons is treated as a random variable to account for the electrophysiological variations across a populations of nearly identical neurons. Employing superstatistical framework, both ISI distribution and sub-threshold membrane potential distribution of neuronal ensemble are obtained in terms of generalized K-distribution...
March 2, 2018: Bio Systems
Vladimir N Binhi
Many migratory animals regularly travel thousands of kilometers, exactly finding their seasonal destinations. The nature of this ability is still not fully understood. The aggregation of animals in groups and their socially coordinated movement is considered a way to eliminate navigational errors. Orientation accuracy of a group may be significantly higher as the errors caused by a variety of casual factors are averaged due to social interactions. This idea, called the "many wrongs principle," has been confirmed both in behavioral experiments and numerical simulations...
March 1, 2018: Bio Systems
Jordi Vallverdú, Oscar Castro, Richard Mayne, Max Talanov, Michael Levin, Frantisek Baluška, Yukio Gunji, Audrey Dussutour, Hector Zenil, Andrew Adamatzky
No abstract text is available yet for this article.
February 24, 2018: Bio Systems
Marjan Faizi, Tomáš Zavrel, Cristina Loureiro, Jan Cerveny, Ralf Steuer
Photoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function typically reduces the proteome available for other cellular functions. Here, we develop a semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation...
February 21, 2018: Bio Systems
Ekaterina Myasnikova, Alexander Spirov
The first manifestation of a segmentation pattern in the early Drosophila development is the formation of expression domains of genes belonging to the gap class. In our previous research the phenomenon of the gap system's robustness, exhibited as the ability to reduce highly variable gene expression in the course of development, was explained as a result of gene cross-regulation. In this paper we formulate the rigorous robustness conditions using the inherent properties of gap gene family. We propose an approach based on the observation that for the formation of a pattern with well-established domain borders it is necessary that there exist a stationary nucleus in which the gene expression level is almost constant in time...
February 8, 2018: Bio Systems
Mahendra Kumar Prajapat, Supreet Saini
Bacteria release signaling molecules into the surrounding environment and sense them when present in their proximity. Using this strategy, a cell estimates the number of neighbors in its surrounding. Upon sensing a critical number of individuals, bacteria coordinate a number of cellular processes. This density-dependent control of gene expression and physiology is called quorum sensing (QS). Quorum sensing controls a wide variety of functions in bacteria, including those related to motility, growth, virulence etc...
February 5, 2018: Bio Systems
Juan J Díaz-Montaña, Francisco Gómez-Vela, Norberto Díaz-Díaz
MOTIVATION: Gene networks are currently considered a powerful tool to model biological processes in the Bioinformatics field. A number of approaches to infer gene networks and various software tools to handle them in a visual simplified way have been developed recently. However, there is still a need to assess the inferred networks in order to prove their relevance. RESULTS: In this paper, we present the new GNC-app for Cytoscape. GNC-app implements the GNC methodology for assessing the biological coherence of gene association networks and integrates it into Cytoscape...
February 2, 2018: Bio Systems
Belkacem Khaldi, Fouzi Harrou, Foudil Cherif, Ying Sun
In certain swarm applications, where the inter-agent distance is not the only factor in the collective behaviours of the swarm, additional properties such as density could have a crucial effect. In this paper, we propose applying a Distance-Weighted K-Nearest Neighbouring (DW-KNN) topology to the behaviour of robot swarms performing self-organized aggregation, in combination with a virtual physics approach to keep the robots together. A distance-weighted function based on a Smoothed Particle Hydrodynamic (SPH) interpolation approach, which is used to evaluate the robot density in the swarm, is applied as the key factor for identifying the K-nearest neighbours taken into account when aggregating the robots...
January 31, 2018: Bio Systems
Mona Arabzadeh, Morteza Saheb Zamani, Mehdi Sedighi, Sayed-Amir Marashi
An Elementary Flux Mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to find a subset of EFMs is proposed based on a graph data model. The given metabolic network is mapped to the graph model and decisions for reaction inclusion can be made based on metabolites and their associated reactions...
January 11, 2018: Bio Systems
Vladimir P Zhdanov
Nanocarrier-mediated mRNA delivery and release into the cells with subsequent translation to protein is of interest in the context of the development of a new generation of drugs. In particular, this protein can play a role of a transcription factor and be used as a tool to regulate temporarily the genetic networks. The corresponding transient kinetics of gene expression are expected to depend on the mechanism and duration of mRNA release. Assuming the release to be rapid on the time scale of other steps, the author shows theoretically the mRNA-related transient features of gene expression occurring in stable, bistable, and oscillatory regimes in a single cell...
January 10, 2018: Bio Systems
Jordi Vallverdú, Oscar Castro, Richard Mayne, Max Talanov, Michael Levin, Frantisek Baluška, Yukio Gunji, Audrey Dussutour, Hector Zenil, Andrew Adamatzky
The slime mould Physarum polycephalum has been used in developing unconventional computing devices for in which the slime mould played a role of a sensing, actuating, and computing device. These devices treated the slime mould rather as an active living substrate yet the slime mould is a self-consistent living creature which evolved for millions of years and occupied most part of the world, but in any case, that living entity did not own true cognition, just automated biochemical mechanisms. To "rehabilitate" the slime mould from the rank of a purely living electronics element to a "creature of thoughts" we are analyzing the cognitive potential of P...
January 8, 2018: Bio Systems
Marco Iosa, Giovanni Morone, Stefano Paolucci
In recent years, there has been a renewed interest in the use of the so-called golden ratio (Phi, ϕ), an irrational number with fractal properties, used in artworks since V century BC. and now for modelling complex biological structures and functions. This number, in fact, recursively pops-up in human history, from Ancient Greeks to Renaissance, and to contemporary scientific studies. Nevertheless, recent scientific results often fall between two extremes: those of a priori sceptic researchers accusing the artificial emergence of ϕ in many studies, and those of researchers that find a mystic meaning in the presence of ϕ in human physiology...
January 6, 2018: Bio Systems
Dorota Formanowicz, Marcin Radom, Agnieszka Rybarczyk, Piotr Formanowicz
The superoxide-driven Fenton reaction plays an important role in the transformation of poorly reactive radicals into highly reactive ones. These highly reactive species (ROS), especially hydroxyl radicals can lead to many disturbances contributing to the endothelial dysfunction being a starting point for atherosclerosis. Although, iron has been identified as a possible culprit influencing formation of ROS, its significance in this process is still debatable. To better understand this phenomenon, the influence of blockade of Fenton reaction in a proposed Petri net-based model of the selected aspects of the iron ROS-induced toxicity in atherosclerosis has been evaluated...
January 6, 2018: Bio Systems
Yoshiaki Nishiyama, Yutaka Saikawa, Nobuaki Nishiyama
Population dynamics of regulatory T cells (Treg) are crucial for the underlying interplay between leukemic and immune cells in progression of acute myeloid leukemia (AML). The goal of this work is to elucidate the dynamics of a model that includes Treg, which can be qualitatively assessed by accumulating clinical findings on the impact of activated immune cell infusion after selective Treg depletion. We constructed an ordinary differential equation model to describe the dynamics of three components in AML: leukemic blast cells, mature regulatory T cells (Treg), and mature effective T cells (Teff), including cytotoxic T lymphocytes...
March 2018: Bio Systems
Peter Dittrich
The organic code concept and its operationalization by molecular codes have been introduced to study the semiotic nature of living systems. This contribution develops further the idea that the semantic capacity of a physical medium can be measured by assessing its ability to implement a code as a contingent mapping. For demonstration and evaluation, the approach is applied to a formal medium: elementary cellular automata (ECA). The semantic capacity is measured by counting the number of ways codes can be implemented...
February 2018: Bio Systems
Kirti Prakash, David Fournier
Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutralisation, molecular specificity, robustness and evolvability. Next, we present evidence for the association among different histone modifications at various levels of chromatin organisation and show how these relationships relate to function such as transcription, replication and cell division...
February 2018: Bio Systems
Luc Steels, Eörs Szathmáry
The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Adopting this perspective has two major benefits...
February 2018: Bio Systems
Marcella Faria
No abstract text is available yet for this article.
February 2018: Bio Systems
Marcello Barbieri
Various independent discoveries have shown that many organic codes exist in living systems, and this implies that they came into being during the history of life and contributed to that history. The genetic code appeared in a population of primitive systems that has been referred to as the common ancestor, and it has been proposed that three distinct signal processing codes gave origin to the three primary kingdoms of Archaea, Bacteria and Eukarya. After the genetic code and the signal processing codes, on the other hand, only the ancestors of the eukaryotes continued to explore the coding space and gave origin to splicing codes, histone code, tubulin code, compartment codes and many others...
February 2018: Bio Systems
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