Complex systems in drug research: II. The ligand-active site-water confluence as a complex system

Complexity ◽  
1996 ◽  
Vol 1 (4) ◽  
pp. 37-42 ◽  
Author(s):  
Lemont B. Kier ◽  
Bernard Testa
Keyword(s):  
Complex System ◽  
Complex Systems ◽  
Active Site ◽  
Drug Research ◽  
Site Water

In-Between and Through: Architecture and Complexity

2005 ◽  
Vol 3 (3) ◽  
pp. 335-354 ◽  
Author(s):  
Clarissa Ribeiro Pereira de Almeida ◽  
Anja Pratschke ◽  
Renata La Rocca
Keyword(s):  
Complex System ◽  
Software Engineering ◽  
Complex Systems ◽  
Design Process ◽  
Three Dimensional ◽  
Self Organization ◽  
Three Dimensional Modeling ◽  
Dimensional Modeling ◽  
Complex Thought ◽  
Basic Characteristics

This paper draws on current research on complexity and design process in architecture and offers a proposal for how architects might bring complex thought to bear on the understanding of design process as a complex system, to understand architecture as a way of organizing events, and of organizing interaction. Our intention is to explore the hypothesis that the basic characteristics of complex systems – emergence, nonlinearity, self-organization, hologramaticity, and so forth – can function as effective tools for conceptualization that can usefully extend the understanding of the way architects think and act throughout the design process. To illustrate the discussions, we show how architects might bring complex thought inside a transdisciplinary design process by using models such as software engineering diagrams, and three-dimensional modeling network environments such as media to integrate, connect and ‘trans–act’.

scholarly journals Toward Reverse Engineering to Economic Analysis: An Overview of Tools and Methodology

2021 ◽  
Author(s):  
Marisa Faggini ◽  
Bruna Bruno ◽  
Anna Parziale
Keyword(s):  
Complex System ◽  
Nonlinear Dynamics ◽  
Economic Analysis ◽  
Complex Systems ◽  
Reverse Engineering ◽  
Underlying Mechanism ◽  
Economic Data ◽  
Agent Based ◽  
Economic Agents ◽  
Advantages And Disadvantages

AbstractFollowing the reverse engineering (RE) approach to analyse an economic complex system is to infer how its underlying mechanism works. The main factors that condition the difficulty of RE are the number of variable components in the system and, most importantly, the interdependence of components on one another and nonlinear dynamics. All those aspects characterize the economic complex systems within which economic agents make their choices. Economic complex systems are adopted in RE science, and they could be used to understand, predict and model the dynamics of the complex systems that enable to define and to control the economic environment. With the RE approach, economic data could be used to peek into the internal workings of the economic complex system, providing information about its underling nonlinear dynamics. The idea of this paper arises from the aim to deepen the comprehension of this approach and to highlight the potential implementation of tools and methodologies based on it to treat economic complex systems. An overview of the literature about the RE is presented, by focusing on the definition and on the state of the art of the research, and then we consider two potential tools that could translate the methodological issues of RE by evidencing advantages and disadvantages for economic analysis: the recurrence analysis and the agent-based model (ABM).

scholarly journals Detection of Emergent Situations in Complex Systems by Structural Invariant (MB, M)

MENDEL ◽  
2017 ◽  
Vol 23 (1) ◽  
pp. 163-170 ◽  
Author(s):  
Jiri Bila ◽  
Martin Novak
Keyword(s):  
Complex System ◽  
Complex Systems ◽  
Detection Method ◽  
Water Cycle ◽  
Ramsey Theorem ◽  
Structural Invariant

The paper introduces complete description of the detection method that uses structural invariant Matroid and its Bases (MB, M). There are recapitulated essential concepts from the used knowledge field as “complex system, emergent situations (A, B, C)”, Ramsey theorem and principal computation variables “power” and “complexity” of emergence phenomenon. The method is explained in details and the demonstration of its application is done by the detection of emergent situation – violation of Short Water Cycle in an ecosystem.

scholarly journals Assessing Cyber-Worthiness of Complex System Capabilities using MBSE: A new rigorous engineering methodology

2021 ◽  
Author(s):  
Stuart Fowler ◽  
Keith Joiner ◽  
Elena Sitnikova
Keyword(s):  
Complex System ◽  
Complex Systems ◽  
Systems Engineering ◽  
Cyber Attacks ◽  
Simulation Methods ◽  
Assessment Methodology ◽  
Cyber Attack ◽  
Cyber Threats ◽  
Attack Surface ◽  
Model Based Systems Engineering

<div>Cyber-worthiness as it is termed in Australian Defence, or cyber-maturity more broadly, is a necessary feature of modern complex systems which are required to operate in a hostile cyber environment. To evaluate the cyber-worthiness of complex systems, an assessment methodology is required to examine a complex system’s or system-of-system’s vulnerability to and risk of cyber-attacks that can compromise such systems. This assessment methodology should address the cyber-attack surface and threat kill chains, including supply chains and supporting infrastructure. A cyber-worthiness capability assessment methodology has been developed based on model-based systems engineering concepts to analyse the cyber-worthiness of complex systems and present a risk assessment of various cyber threats to the complex system. This methodology incorporates modelling and simulation methods that provide organisations greater visibility and consistency across diverse systems, especially to drive cybersecurity controls, investment and operational decisions involving aggregated systems. In this paper, the developed methodology will be presented in detail and hypothesised outcomes will be discussed.</div>

scholarly journals Relebactam Is a Potent Inhibitor of the KPC-2 β-Lactamase and Restores Imipenem Susceptibility in KPC-Producing Enterobacteriaceae

2018 ◽  
Vol 62 (6) ◽  
Author(s):  
Krisztina M. Papp-Wallace ◽  
Melissa D. Barnes ◽  
Jim Alsop ◽  
Magdalena A. Taracila ◽  
Christopher R. Bethel ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Rate Constant ◽  
Active Site ◽  
Klebsiella Oxytoca ◽  
Enterobacter Aerogenes ◽  
Clinical Isolates ◽  
Piperidine Ring ◽  
Water Molecules ◽  
Content Type ◽  
Site Water

ABSTRACT The imipenem-relebactam combination is in development as a potential treatment regimen for infections caused by Enterobacteriaceae possessing complex β-lactamase backgrounds. Relebactam is a β-lactamase inhibitor that possesses the diazabicyclooctane core, as in avibactam; however, the R1 side chain of relebactam also includes a piperidine ring, whereas that of avibactam is a carboxyamide. Here, we investigated the inactivation of the Klebsiella pneumoniae carbapenemase KPC-2, the most widespread class A carbapenemase, by relebactam and performed susceptibility testing with imipenem-relebactam using KPC-producing clinical isolates of Enterobacteriaceae . MIC measurements using agar dilution methods revealed that all 101 clinical isolates of KPC-producing Enterobacteriaceae ( K. pneumoniae , Klebsiella oxytoca , Enterobacter cloacae , Enterobacter aerogenes , Citrobacter freundii , Citrobacter koseri , and Escherichia coli ) were highly susceptible to imipenem-relebactam (MICs ≤ 2 mg/liter). Relebactam inhibited KPC-2 with a second-order onset of acylation rate constant ( k 2 / K ) value of 24,750 M −1 s −1 and demonstrated a slow off-rate constant ( k off ) of 0.0002 s −1 . Biochemical analysis using time-based mass spectrometry to map intermediates revealed that the KPC-2–relebactam acyl-enzyme complex was stable for up to 24 h. Importantly, desulfation of relebactam was not observed using mass spectrometry. Desulfation and subsequent deacylation have been observed during the reaction of KPC-2 with avibactam. Upon molecular dynamics simulations of relebactam in the KPC-2 active site, we found that the positioning of active-site water molecules is less favorable for desulfation in the KPC-2 active site than it is in the KPC-2–avibactam complex. In the acyl complexes, the water molecules are within 2.5 to 3 Å of the avibactam sulfate; however, they are more than 5 to 6 Å from the relebactam sulfate. As a result, we propose that the KPC-2–relebactam acyl complex is more stable than the KPC-2–avibactam complex. The clinical implications of this difference are not currently known.

Industry 4.0 From the Systems Engineering Perspective

2020 ◽  
pp. 575-599
Author(s):  
Vladimír Bureš
Keyword(s):  
Complex System ◽  
Physical Activity ◽  
Complex Systems ◽  
Frequency Analysis ◽  
Systems Engineering ◽  
Industry 4.0 ◽  
Control Level ◽  
Design Development ◽  
Starting Point ◽  
And Control

Systems engineering focuses on design, development, and implementation of complex systems. Not only does the Industry 4.0 concept consist of various technical components that need to be properly set and interconnected, but it is also tied to various managerial aspects. Thus, systems engineering approach can be used for its successful deployment. Overemphasis of technological aspects of Industry 4.0 represents the main starting point of this chapter. Then, collocation analysis, word clusters identification, selection and exemplification of selected domain in the business management realm, and frequency analysis are used in order to develop a holistic framework of Industry 4.0. This framework comprises six levels – physical, activity, outcome, content, triggers, and context. Moreover, the information and control level is integrated. The new holistic framework helps to consider Industry 4.0 from the complex systems engineering perspective – design and deployment of a complex system with required parameters and functionality.

Cellular Automata

2008 ◽  
pp. 57-84 ◽  
Author(s):  
Terry Bossomaier
Keyword(s):  
Complex System ◽  
Cellular Automata ◽  
Complex Systems ◽  
Lava Flows ◽  
Edge Of Chaos ◽  
Complex Systems Modelling ◽  
Systems Modelling ◽  
Theoretical Issues

In this chapter we present a view of cellular automata (CAs) as the quintessential complex system and how they can be used for complex systems modelling. First we consider theoretical issues of the complexity of their behaviour, discussing the Wolfram Classification, the Langton, lambda parameter and the edge of chaos. Then we consider the input entropy as a way of quantifying complex rules. Finally we contrast explicit CA modelling of geophysical systems with heuristic particle based methods for the visualisation of lava flows.

Complexity and Criticality

2020 ◽  
pp. 42-50
Author(s):  
Helmut Satz
Keyword(s):  
Complex System ◽  
Complex Systems ◽  
Critical Point ◽  
Correlation Length ◽  
Critical Behavior ◽  
Scale Free ◽  
Self Organized ◽  
Self Organized Criticality ◽  
Free Behavior

Complex systems and critical behavior in complex system are defined in terms of correlation between constituents in the medium, subject to screening by intermediate constituents. At a critical point, the correlation length diverges—as a result, one finds the scale-free behavior also observed for bird flocks. This behavior is therefore possibly a form of self-organized criticality.

Human Understanding of Complex Systems

2018 ◽  
Author(s):  
James A. Anderson
Keyword(s):  
Complex System ◽  
Complex Systems ◽  
20Th Century ◽  
Brain Function ◽  
Hydraulic System ◽  
17Th Century ◽  
Hydraulic Systems ◽  
Detailed Model ◽  
Human Understanding ◽  
The Brain

An important tool for understanding new and complex systems is analogy. Analogies to brain function are often the most complex systems of the time. In the 17th century, complex hydraulic systems were common. Descartes proposed a detailed model of the brain based on a hydraulic system. In the 19th and 20th centuries, the telephone and telegraph systems were used as brain analogies. This analogy is useful for understanding system connectivity constraints and the practical need for a central exchange (“brain”) for switching and memory. An extreme version of the central exchange analogy was called behaviorism or S-R psychology, popular in the first half of the 20th century. Obvious problems with analogy are its basic untruth and a tendency for a complex system to be thought of as magic if its technological roots are lost.

scholarly journals The Complexity of the Homeopathic Healing Response Part 2: The Role of the Homeopathic Simillimum as a Complex System in Initiating Recovery from Disease

Homeopathy ◽  
2019 ◽  
Vol 109 (02) ◽  
pp. 051-064 ◽  
Author(s):  
Iris R. Bell
Keyword(s):  
Complex System ◽  
Quantum Dots ◽  
Complex Systems ◽  
Protein Corona ◽  
Low Doses ◽  
Adaptive Responses ◽  
Homeopathic Medicine ◽  
Nano Structures ◽  
Complex Adaptive ◽  
Source Materials

Abstract Background Evidence indicates that homeopathic medicines are complex self-organizing nano-scale systems that generate unique low-intensity electromagnetic signals and/or quantum coherence domains. In Part 1, we reviewed relevant concepts from complex adaptive systems science on living systems for the nature of homeopathic healing. Aim In Part 2, we discuss the complex-system nature of homeopathic medicines. The aim is to relate the evidence on the nature and properties of homeopathic medicines to the complex systems model for homeopathic healing. Methods and Results The work is a narrative review, with complexity model development for the nature of homeopathic medicines. Studies suggest that homeopathic manufacturing generates nano-structures of source material, silica and silicon quantum dots if succussed in glassware or including botanical source materials; or carbon quantum dots if succussed in plastic or including any organic source materials, as well as solute-induced water nano-structures carrying medicine-specific information. On contact with physiological fluids (e.g., blood plasma), there is evidence that nano-structures additionally adsorb individualized patterns of the recipient's own proteins on to their surfaces to create a unique protein corona coat (shell). Thus, the simillimum may generate a personalized biological identity upon administration. Consequently, a medicine can serve as an individually salient, self-similar information carrier, whose protein corona constituent pattern reflects the individual's current internal state of health/disease. Homeopathic medicine complexity emerges from interactions of the component parts from source, silica from glassware or carbon from plastic containers, solvents (lactose, water, ethanol), adsorbed biomolecule layers from plant or animal sources, and adsorbed biomolecules of the recipient. Low doses of these complex medicines can act as biological signaling agents to initiate hormesis via a network-wide pattern of adaptive responses by the recipient complex adaptive system, rather than as conventional pharmaceutical drugs. Biological mediators of adaptive responses include inter-connected network elements of the cell danger/damage defense system: for example, gene expression, reactive oxygen species, heat shock proteins, cytokines, macrophages, T-cells, and associated brain–immune system mediator pathways. Conclusions Every homeopathic medicine is a complex nano-scale system involving multiple inter-connected, interacting components, and emergent properties. Simillimum individualization derives from formation of a unique personalized protein corona shell adsorbed to the reactive surface of the homeopathic nano-structures on contact with the recipient's body fluids. Low doses of such complex nano-structures initiate the adaptive processes of hormesis to mobilize endogenous healing of a disease state. The capacity for self-organization and self-similarity in complex systems is the key to future research on the nature of homeopathic medicines and systemic healing during individualized homeopathic treatment.

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