scholarly journals Role of Combinatorial Complexity in Genetic Networks

2019 ◽  
Vol 4 (Spring 2019) ◽  
Author(s):  
Sharon Yang
Keyword(s):  
Complex Formation ◽  
Differential Equations ◽  
Mathematical Models ◽  
Feedback Loops ◽  
Genetic Networks ◽  
Combinatorial Complexity ◽  
Generic Models ◽  
Common Motif ◽  
Intermediate States

A common motif found in genetic networks is the formation of large complexes. One difficulty in modeling this motif is the large number of possible intermediate complexes that can form. For instance, if a complex could contain up to 10 different proteins, 210 possible intermediate complexes can form. Keeping track of all complexes is difficult and often ignored in mathematical models. Here we present an algorithm to code ordinary differential equations (ODEs) to model genetic networks with combinatorial complexity. In these routines, the general binding rules, which counts for the majority of the reactions, are implemented automatically, thus the users only need to code a few specific reaction rules. Using this algorithm, we find that the behavior of these models depends greatly on the specific rules of complex formation. Through simulating three generic models for complex formation, we find that these models show widely different timescales, distribution of intermediate states, and ability to promote oscillations within feedback loops. These results provide tools for the incorporation of combinatorial complexity of genetic networks and show how this incorporation may be vital to accurately predict the network dynamics.

Pieces of Mind

2018 ◽  
Author(s):  
Carrie Figdor
Keyword(s):  
Mathematical Models ◽  
Moral Status ◽  
Entire Range ◽  
Fruit Flies ◽  
Literal Interpretation ◽  
Psychological Capacities

Many people accept that chimpanzees, dolphins, and some other animals can think and feel. But these cases are just the tip of a growing iceberg. If biologists are right, fruit flies and plants make decisions, worms and honeybees can be trained, bacteria communicate linguistically, and neurons have preferences. Just how far does cognition go? This book is the first to critically consider this question from the perspective of the entire range of new ascriptions of psychological capacities throughout biology. It is also the first to consider the role of mathematical models and other quantitative forms of evidence in prompting and supporting the new ascriptions. It defends a default literal interpretation of psychological terms across biological domains. It also considers the implications of the literal view for efforts to explain the mind’s place in nature and for traditional ways of distinguishing the superior moral status of humans relative to other living beings.

scholarly journals An optical biosensor study of the interaction parameters and role of hydrophobic tails of cytochrome P450 2B4, b5 and NADPH-flavoprotein in complex formation

IUBMB Life ◽  
1997 ◽  
Vol 42 (4) ◽  
pp. 731-737 ◽  
Author(s):  
Yuriy Ivanov ◽  
Irina Kanaeva ◽  
Michail Eldarov ◽  
Konstantin Sklyabin ◽  
Michael Lehnerer ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Complex Formation ◽  
Optical Biosensor ◽  
Interaction Parameters ◽  
Cytochrome P450 2B4

scholarly journals Simple mathematical models for controlling COVID-19 transmission through social distancing and community awareness

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Ahmed S. Elgazzar
Keyword(s):  
Mathematical Models ◽  
Virus Transmission ◽  
Small World ◽  
Vaccination Rate ◽  
The Novel ◽  
Social Distancing ◽  
Community Awareness ◽  
Sufficient Degree ◽  
And Control

Abstract The novel COVID-19 pandemic is a current, major global health threat. Up till now, there is no fully approved pharmacological treatment or a vaccine. Also, its origin is still mysterious. In this study, simple mathematical models were employed to examine the dynamics of transmission and control of COVID-19 taking into consideration social distancing and community awareness. Both situations of homogeneous and nonhomogeneous population were considered. Based on the calculations, a sufficient degree of social distancing based on its reproductive ratio is found to be effective in controlling COVID-19, even in the absence of a vaccine. With a vaccine, social distancing minimizes the sufficient vaccination rate to control the disease. Community awareness also has a great impact in eradicating the virus transmission. The model is simulated on small-world networks and the role of social distancing in controlling the infection is explained.

scholarly journals On attracting sets in artificial networks: cross activation

2018 ◽  
Vol 16 ◽  
pp. 01005
Author(s):  
Felix Sadyrbaev
Keyword(s):  
Dynamical Systems ◽  
Differential Equations ◽  
Mathematical Models ◽  
Ordinary Differential Equations ◽  
Critical Points ◽  
Regulatory Networks ◽  
Main Diagonal ◽  
Sigmoidal Function ◽  
Genomic Regulatory Networks ◽  
Over Time

Mathematical models of artificial networks can be formulated in terms of dynamical systems describing the behaviour of a network over time. The interrelation between nodes (elements) of a network is encoded in the regulatory matrix. We consider a system of ordinary differential equations that describes in particular also genomic regulatory networks (GRN) and contains a sigmoidal function. The results are presented on attractors of such systems for a particular case of cross activation. The regulatory matrix is then of particular form consisting of unit entries everywhere except the main diagonal. We show that such a system can have not more than three critical points. At least n–1 eigenvalues corresponding to any of the critical points are negative. An example for a particular choice of sigmoidal function is considered.

scholarly journals Impact of Quantum Dot Surface on Complex Formation with Chlorin e6 and Photodynamic Therapy

Nanomaterials ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 9 ◽  
Author(s):  
Artiom Skripka ◽  
Dominyka Dapkute ◽  
Jurga Valanciunaite ◽  
Vitalijus Karabanovas ◽  
Ricardas Rotomskis
Keyword(s):  
Photodynamic Therapy ◽  
Cancer Therapy ◽  
Complex Formation ◽  
Chemical Properties ◽  
Disease Diagnosis ◽  
Chlorin E6 ◽  
Deep Tissue ◽  
Physico Chemical

Nanomaterials have permeated various fields of scientific research, including that of biomedicine, as alternatives for disease diagnosis and therapy. Among different structures, quantum dots (QDs) have distinctive physico-chemical properties sought after in cancer research and eradication. Within the context of cancer therapy, QDs serve the role of transporters and energy donors to photodynamic therapy (PDT) drugs, extending the applicability and efficiency of classic PDT. In contrast to conventional PDT agents, QDs’ surface can be designed to promote cellular targeting and internalization, while their spectral properties enable better light harvesting and deep-tissue use. Here, we investigate the possibility of complex formation between different amphiphilic coating bearing QDs and photosensitizer chlorin e6 (Ce6). We show that complex formation dynamics are dependent on the type of coating—phospholipids or amphiphilic polymers—as well as on the surface charge of QDs. Förster’s resonant energy transfer occurred in every complex studied, confirming the possibility of indirect Ce6 excitation. Nonetheless, in vitro PDT activity was restricted only to negative charge bearing QD-Ce6 complexes, correlating with better accumulation in cancer cells. Overall, these findings help to better design such and similar complexes, as gained insights can be straightforwardly translated to other types of nanostructures—expanding the palette of possible therapeutic agents for cancer therapy.

scholarly journals Iron Requirement for Mn(II) Oxidation by Leptothrix discophora SS-1

2008 ◽  
Vol 75 (5) ◽  
pp. 1229-1235 ◽  
Author(s):  
Iman A. El Gheriany ◽  
Daniela Bocioaga ◽  
Anthony G. Hay ◽  
William C. Ghiorse ◽  
Michael L. Shuler ◽  
...  
Keyword(s):  
Complex Formation ◽  
Temporal Variations ◽  
Iron Limitation ◽  
Gene Transcript ◽  
Cellular Functions ◽  
Transcript Levels ◽  
Leptothrix Discophora ◽  
Geochemical Cycling ◽  
Iron Requirement

ABSTRACT A common form of biocatalysis of Mn(II) oxidation results in the formation of biogenic Mn(III, IV) oxides and is a key reaction in the geochemical cycling of Mn. In this study, we grew the model Mn(II)-oxidizing bacterium Leptothrix discophora SS-1 in media with limited iron (0.1 μM iron/5.8 mM pyruvate) and sufficient iron (0.2 μM iron/5.8 mM pyruvate). The influence of iron on the rate of extracellular Mn(II) oxidation was evaluated. Cultures in which cell growth was limited by iron exhibited reduced abilities to oxidize Mn(II) compared to cultures in medium with sufficient iron. While the extracellular Mn(II)-oxidizing factor (MOF) is thought to be a putative multicopper oxidase, Mn(II) oxidation in the presence of zero added Cu(II) was detected and the decrease in the observed Mn(II) oxidation rate in iron-limited cultures was not relieved when the medium was supplemented with Cu(II). The decline of Mn(II) oxidation under iron-limited conditions was not accompanied by siderophore production and is unlikely to be an artifact of siderophore complex formation with Mn(III). The temporal variations in mofA gene transcript levels under conditions of limited and abundant iron were similar, indicating that iron limitation did not interfere with the transcription of the mofA gene. Our quantitative PCR results provide a step forward in understanding the regulation of Mn(II) oxidation. The mechanistic role of iron in Mn(II) oxidation is uncertain; the data are consistent with a direct requirement for iron as a component of the MOF or an indirect effect of iron resulting from the limitation of one of many cellular functions requiring iron.

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