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https://www.readbyqxmd.com/read/28924178/logical-gates-in-actin-monomer
#1
Andrew Adamatzky
We evaluate information processing capacity of a single actin molecule by calculating distributions of logical gates implemented by the molecule via propagating patterns of excitation. We represent a filamentous actin molecule as an excitable automaton network (F-actin automaton). where every atom updates its state depending on states of atoms its connected to with chemical bonds (hard neighbours) and atoms being in physical proximity to the atom (soft neighbours). A resting atom excites if a sum of its excited hard neighbours and a weighted sum of its soft neighbours belong to some specified interval...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916462/causation-constructors-and-codes
#2
Jan-Hendrik S Hofmeyr
Relational biology relies heavily on the enriched understanding of causal entailment that Robert Rosen's formalisation of Aristotle's four causes has made possible, although to date efficient causes and the rehabilitation of final cause have been its main focus. Formal cause has been paid rather scant attention, but, as this paper demonstrates, is crucial to our understanding of many types of processes, not necessarily biological. The graph-theoretic relational diagram of a mapping has played a key role in relational biology, and the first part of the paper is devoted to developing an explicit representation of formal cause in the diagram and how it acts in combination with efficient cause to form a mapping...
September 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/28911878/comparison-of-proposed-countermeasures-for-dilemma-zone-at-signalized-intersections-based-on-cellular-automata-simulations
#3
Yina Wu, Mohamed Abdel-Aty, Yaoxian Ding, Bin Jia, Qi Shi, Xuedong Yan
The Type II dilemma zone describes the road segment to a signalized intersection where drivers have difficulties to decide either stop or go at the onset of yellow signal. Such phenomenon can result in an increased crash risk at signalized intersections. Different types of warning systems have been proposed to help drivers make decisions. Although the warning systems help to improve drivers' behavior, they also have several disadvantages such as increasing rear-end crashes or red-light running (RLR) violations...
September 11, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28846712/hybrid-multiscale-modeling-and-prediction-of-cancer-cell-behavior
#4
Mohammad Hossein Zangooei, Jafar Habibi
BACKGROUND: Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. METHODS: In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods...
2017: PloS One
https://www.readbyqxmd.com/read/28841563/simultaneous-observation-of-hybrid-states-for-cyber-physical-systems-a-case-study-of-electric-vehicle-powertrain
#5
Chen Lv, Yahui Liu, Xiaosong Hu, Hongyan Guo, Dongpu Cao, Fei-Yue Wang
As a typical cyber-physical system (CPS), electrified vehicle becomes a hot research topic due to its high efficiency and low emissions. In order to develop advanced electric powertrains, accurate estimations of the unmeasurable hybrid states, including discrete backlash nonlinearity and continuous half-shaft torque, are of great importance. In this paper, a novel estimation algorithm for simultaneously identifying the backlash position and half-shaft torque of an electric powertrain is proposed using a hybrid system approach...
August 22, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28814968/asp-based-method-for-the-enumeration-of-attractors-in-non-deterministic-synchronous-and-asynchronous-multi-valued-networks
#6
Emna Ben Abdallah, Maxime Folschette, Olivier Roux, Morgan Magnin
BACKGROUND: This paper addresses the problem of finding attractors in biological regulatory networks. We focus here on non-deterministic synchronous and asynchronous multi-valued networks, modeled using automata networks (AN). AN is a general and well-suited formalism to study complex interactions between different components (genes, proteins,...). An attractor is a minimal trap domain, that is, a part of the state-transition graph that cannot be escaped. Such structures are terminal components of the dynamics and take the form of steady states (singleton) or complex compositions of cycles (non-singleton)...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28748205/dataset-demonstrating-the-temperature-effect-on-average-output-polarization-for-qca-based-reversible-logic-gates
#7
Md Kamrul Hassan, Nur Mohammad Nahid, Ali Newaz Bahar, Mohammad Maksudur Rahman Bhuiyan, Md Abdullah-Al-Shafi, Kawsar Ahmed
Quantum-dot cellular automata (QCA) is a developing nanotechnology, which seems to be a good candidate to replace the conventional complementary metal-oxide-semiconductor (CMOS) technology. In this article, we present the dataset of average output polarization (AOP) for basic reversible logic gates presented in Ali Newaz et al. (2016) [1]. QCADesigner 2.0.3 has been employed to analysis the AOP of reversible gates at different temperature levels in Kelvin (K) unit.
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28736575/identification-of-bifurcation-transitions-in-biological-regulatory-networks-using-answer-set-programming
#8
Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, Loïc Paulevé
BACKGROUND: Numerous cellular differentiation processes can be captured using discrete qualitative models of biological regulatory networks. These models describe the temporal evolution of the state of the network subject to different competing transitions, potentially leading the system to different attractors. This paper focusses on the formal identification of states and transitions that are crucial for preserving or pre-empting the reachability of a given behaviour. METHODS: In the context of non-deterministic automata networks, we propose a static identification of so-called bifurcations, i...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28721495/diversity-and-survival-of-artificial-lifeforms-under-sedimentation-and-random-motion
#9
Nicolas Glade, Olivier Bastien, Pascal Ballet
Cellular automata are often used to explore the numerous possible scenarios of what could have occurred at the origins of life and before, during the prebiotic ages, when very simple molecules started to assemble and organise into larger catalytic or informative structures, or to simulate ecosystems. Artificial self-maintained spatial structures emerge in cellular automata and are often used to represent molecules or living organisms. They converge generally towards homogeneous stationary soups of still-life creatures...
July 18, 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28705234/in-silico-characterization-of-cell-cell-interactions-using-a-cellular-automata-model-of-cell-culture
#10
Takanori Kihara, Kosuke Kashitani, Jun Miyake
BACKGROUND: Cell proliferation is a key characteristic of eukaryotic cells. During cell proliferation, cells interact with each other. In this study, we developed a cellular automata model to estimate cell-cell interactions using experimentally obtained images of cultured cells. RESULTS: We used four types of cells; HeLa cells, human osteosarcoma (HOS) cells, rat mesenchymal stem cells (MSCs), and rat smooth muscle A7r5 cells. These cells were cultured and stained daily...
July 14, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28696316/light-mediated-self-organization-of-sunflower-stands-increases-oil-yield-in-the-field
#11
Mónica López Pereira, Victor O Sadras, William Batista, Jorge J Casal, Antonio J Hall
Here, we show a unique crop response to intraspecific interference, whereby neighboring sunflower plants in a row avoid each other by growing toward a more favorable light environment and collectively increase production per unit land area. In high-density stands, a given plant inclined toward one side of the interrow space, and the immediate neighbors inclined in the opposite direction. This process started early as an incipient inclination of pioneer plants, and the arrangement propagated gradually as a "wave" of alternate inclination that persisted until maturity...
July 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28680654/a-quantum-samaritan-s-dilemma-cellular-automaton
#12
Ramón Alonso-Sanz, Haozhen Situ
The dynamics of a spatial quantum formulation of the iterated Samaritan's dilemma game with variable entangling is studied in this work. The game is played in the cellular automata manner, i.e. with local and synchronous interaction. The game is assessed in fair and unfair contests, in noiseless scenarios and with disrupting quantum noise.
June 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28671565/efficient-depth-enhancement-using-a-combination-of-color-and-depth-information
#13
Kyungjae Lee, Yuseok Ban, Sangyoun Lee
Studies on depth images containing three-dimensional information have been performed for many practical applications. However, the depth images acquired from depth sensors have inherent problems, such as missing values and noisy boundaries. These problems significantly affect the performance of applications that use a depth image as their input. This paper describes a depth enhancement algorithm based on a combination of color and depth information. To fill depth holes and recover object shapes, asynchronous cellular automata with neighborhood distance maps are used...
July 1, 2017: Sensors
https://www.readbyqxmd.com/read/28618473/approximate-probabilistic-cellular-automata-for-the-dynamics-of-single-species-populations-under-discrete-logisticlike-growth-with-and-without-weak-allee-effects
#14
J Ricardo G Mendonça, Yeva Gevorgyan
We investigate one-dimensional elementary probabilistic cellular automata (PCA) whose dynamics in first-order mean-field approximation yields discrete logisticlike growth models for a single-species unstructured population with nonoverlapping generations. Beginning with a general six-parameter model, we find constraints on the transition probabilities of the PCA that guarantee that the ensuing approximations make sense in terms of population dynamics and classify the valid combinations thereof. Several possible models display a negative cubic term that can be interpreted as a weak Allee factor...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28617348/urban-ecological-security-simulation-and-prediction-using-an-improved-cellular-automata-ca-approach-a-case-study-for-the-city-of-wuhan-in-china
#15
Yuan Gao, Chuanrong Zhang, Qingsong He, Yaolin Liu
Ecological security is an important research topic, especially urban ecological security. As highly populated eco-systems, cities always have more fragile ecological environments. However, most of the research on urban ecological security in literature has focused on evaluating current or past status of the ecological environment. Very little literature has carried out simulation or prediction of future ecological security. In addition, there is even less literature exploring the urban ecological environment at a fine scale...
June 15, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28608625/computing-in-verotoxin
#16
Andrew Adamatzky
We develop an excitable automata model of a protein verotoxin and demonstrate that logic gates and circuits are realised in the model via interacting patterns of excitation. By sampling potential input pairs of nodes, we calculate frequencies of logic gates which occurred in the verotoxin model for various parameters of node excitation rules. We show that overall the gates can be arranged in the following hierarchy of descending frequencies: AND>OR>AND-NOT>XOR. We demonstrate realisations of one-bit half-adder and controlled-not gates and estimate memory capacity of the verotoxin molecule...
June 13, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28540852/association-of-polyunsaturated-saturated-fatty-acids-to-metabolic-syndrome-cardiovascular-risk-factors-and-lipoprotein-a-in-hypertensive-type-2-diabetic-patients
#17
Amira Fatma Bennacer, Elmahdi Haffaf, Ghouti Kacimi, Brahim Oudjit, Elhadj-Ahmed Koceir
The interactions between fatty acids (FA) classes: polyunsaturated (PUFA-ω6, PUFA-ω3), saturated (SFA), EPA (eicosapentaenoic acid-ω3), DHA (docosahexaenoic-ω3) and cardiometabolic syndrome (CMS) clusters, thrombosis development and vascular inflammation are subtle. This relationship is mediated by insulin resistance (IR), endothelial dysfunction, platelet aggregation disorder and atherosclerosis. OBJECTIVES: We investigated whether PUFA/SFA - PUFA-ω6/PUFA-ω3 ratios and EPA + DHA can be associated with predictive atherothrombogenic biomarkers status in type 2 diabetes (T2D) patients with or without hypertension (HT)...
June 1, 2017: Annales de Biologie Clinique
https://www.readbyqxmd.com/read/28536438/optimizing-radiotherapy-protocols-using-computer-automata-to-model-tumour-cell-death-as-a-function-of-oxygen-diffusion-processes
#18
Perrine Paul-Gilloteaux, Vincent Potiron, Grégory Delpon, Stéphane Supiot, Sophie Chiavassa, François Paris, Sylvain V Costes
The concept of hypofractionation is gaining momentum in radiation oncology centres, enabled by recent advances in radiotherapy apparatus. The gain of efficacy of this innovative treatment must be defined. We present a computer model based on translational murine data for in silico testing and optimization of various radiotherapy protocols with respect to tumour resistance and the microenvironment heterogeneity. This model combines automata approaches with image processing algorithms to simulate the cellular response of tumours exposed to ionizing radiation, modelling the alteration of oxygen permeabilization in blood vessels against repeated doses, and introducing mitotic catastrophe (as opposed to arbitrary delayed cell-death) as a means of modelling radiation-induced cell death...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28531644/safety-evaluation-of-driver-cognitive-failures-and-driving-errors-on-right-turn-filtering-movement-at-signalized-road-intersections-based-on-fuzzy-cellular-automata-fca-model
#19
Chen Chai, Yiik Diew Wong, Xuesong Wang
This paper proposes a simulation-based approach to estimate safety impact of driver cognitive failures and driving errors. Fuzzy Logic, which involves linguistic terms and uncertainty, is incorporated with Cellular Automata model to simulate decision-making process of right-turn filtering movement at signalized intersections. Simulation experiments are conducted to estimate the relationships between cognitive failures and driving errors with safety performance. Simulation results show Different types of cognitive failures are found to have varied relationship with driving errors and safety performance...
July 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28529345/compositional-schedulability-analysis-of-real-time-actor-based-systems
#20
Mohammad Mahdi Jaghoori, Frank de Boer, Delphine Longuet, Tom Chothia, Marjan Sirjani
We present an extension of the actor model with real-time, including deadlines associated with messages, and explicit application-level scheduling policies, e.g.,"earliest deadline first" which can be associated with individual actors. Schedulability analysis in this setting amounts to checking whether, given a scheduling policy for each actor, every task is processed within its designated deadline. To check schedulability, we introduce a compositional automata-theoretic approach, based on maximal use of model checking combined with testing...
2017: Acta Informatica
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