Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies (...) for treating diseases such as cancers, is pointed out. The roles played by multiple metastable states in the “continuous uphill flow of Life” supported through internal bioenergetic processes that are coupled to essential inflows are also discussed in relation to dynamic realizations of (M,R)-systems. Furthermore, the roles played by the underlying, many-valued, quantum logics and symbolic computations for ultra-complex biological systems are also briefly discussed. (shrink)

Which function is computed by a Turing machine will depend on how the symbols it manipulates are interpreted. Further, by invoking bizarre systems of notation it is easy to define Turing machines that compute textbook examples of uncomputable functions, such as the solution to the decision problem for first-order logic. Thus, the distinction between computable and uncomputable functions depends on the system of notation used. This raises the question: which systems of notation are the relevant ones for determining (...) whether a function is computable? These are the acceptable notations. I argue for a use criterion of acceptability: the acceptable notations for a domain of objects D\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathcal {D}}$$\end{document} are the notations that we can use for the usual D\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathcal {D}}$$\end{document}-activities. Acceptable notations for natural numbers are ones that we can count with. Acceptable notations for logical formulas are the ones that we can use in inference and logical analysis. And so on. This criterion makes computability a relative notion—whether a function is computable depends on which notations are acceptable, which is relative to our interests and abilities. I argue that this is not a problem, however, since there is independent reason for taking the extension of computable function to be relative to contingent facts. Similarly, the fact that the use criterion makes a mathematical distinction depend on practical concerns is also not a problem because it dovetails with similar phenomena in other areas of computability theory, namely the roles of notation in computation over real numbers and of Extended Church’s Thesis in complexity theory. (shrink)

Tasked with the challenge to build better and better computers, quantum computing and classical computing face the same conundrum: the success of classical computing systems. Small quantum computing systems have been demonstrated, and intermediate-scale systems are on the horizon, capable of calculating numeric results or simulating physical systems far beyond what humans can do by hand. However, to be commercially viable, they must surpass what our wildly successful, highly advanced classical computers can (...) already do. At the same time, those classical computers continue to advance, but those advances are now constrained by thermodynamics, and will soon be limited by the discrete nature of atomic matter and ultimately quantum effects. Technological advances benefit both quantum and classical machinery, altering the competitive landscape. Can we build quantum computing systems that out-compute classical systems capable of some \(10^{30}\) logic gates per month? This article will discuss the interplay in these competing and cooperating technological trends. (shrink)

Energy contributes significantly in almost all aspects of human life as well as economic activities and plays a crucial role in the infrastructural development of a county to alleviate poverty. Generating energy from a renewable source such as small hydropower through the application of pump operating as a turbine mode called Pump as Turbine is one of the best alternatives to provide clean and inexpensive energy. Using Pump as Turbine helps in generating reasonably priced hydroelectric power for communities in underdeveloped (...) counties. This study investigates the effects of internal flow behaviour and performance of Pump as Turbine under different rotational speed and flow rate. The rotational speed is an essential physical parameter as it affects the Pump as Turbine operation. A model-specific speed centrifugal pump model with head 32, flow rate of 12.5 and the rotational speed of 2900 rpm, has been selected for the study. Numerical simulations have been conducted using the k-ω turbulence model to solve three-dimensional equations. The pump mode experimental data were used to confirm the results for better analysis. The results predicted that vortex and turbulent kinetic energy increase per rotational speed increase. Also, at the higher rotational speed, very high recirculation of flow is detected at the blade suction chamber, although the pressure side has a smooth flow. This study provides beneficial information which will serve as a reference to help improve PAT performance along with selecting PAT for a small hydropower site. Future works will consider the impact of blade thickness and cavitation in Pump as Turbine. (shrink)

We consider processes of emergence within the conceptual framework of the Information Loss principle and the concepts of systems conserving information; systems compressing information; and systems amplifying information. We deal with the supposed incompatibility between emergence and computability tout-court. We distinguish between computational emergence, when computation acquires properties, and emergent computation, when computation emerges as a property. The focus is on emergence processes occurring within computational processes. Violations of Turing-computability such as non-explicitness and incompleteness (...) are intended to represent partially the properties of phenomenological emergence, such as logical openness, given by the observer’s cognitive role; structural dynamics where change regards rules rather than only values; and multi-modelling where multiple non-equivalent models are required to model such structural dynamics. In this way, we validate, from an epistemological viewpoint, models and simulations of phenomenological emergence where the sequence of events constitutes the natural, analogical non-Turing computation which a cognitive complex system can reproduce through learning. Reproducibility through learning is different from Turing-like computational iteration. This paper aims to open a new, non-reductionist understanding of the conceptual relationship between emergence and computability. (shrink)

The main claim of this paper is that notions of implementation based on an isomorphic correspondence between physical and computational states are not tenable. Rather, ``implementation'' has to be based on the notion of ``bisimulation'' in order to be able to block unwanted implementation results and incorporate intuitions from computational practice. A formal definition of implementation is suggested, which satisfies theoretical and practical requirements and may also be used to make the functionalist notion of ``physical realization'' precise. The upshot of (...) this new definition of implementation is that implementation cannot distinguish isomorphic bisimilar from non-isomporphic bisimilar systems anymore, thus driving a wedge between the notions of causal and computational complexity. While computationalism does not seem to be affected by this result, the consequences for functionalism are not clear and need further investigations. (shrink)

Church's thesis, that all reasonable definitions of “computability” are equivalent, is not usually thought of in terms of computability by acontinuouscomputer, of which the general-purpose analog computer (GPAC) is a prototype. Here we prove, under a hypothesis of determinism, that the analytic outputs of aC∞GPAC are computable by a digital computer.In [POE, Theorems 5, 6, 7, and 8], Pour-El obtained some related results. (The proof there of Theorem 7 depends on her Theorem 2, for which the proof in [POE] is (...) incorrect, but for which a correct proof is given in [LIR]. Also, the proof in [POE] of Theorem 8 depends on the unproved assertion that a solution of an algebraic differential equation must be analytic on an open subset of its domain. However, this assertion was later proved in [BRR].) As in [POE], we reduce the problem to a problem about solutions of certain systems of algebraic differential equations (ADE's). If such a system is nonsingular (i.e. if the “separant” does not vanish along the given solution), then the argument is very easy (see [VSD] for an even simpler situation), so that the essential difficulties arise fromsingularsystems. Our main tools in handling these difficulties are drawn from the excellent (and difficult) paper [DEL] by Denef and Lipshitz. The author especially wants to thank Leonard Lipshitz for his kind help in the preparation of the present paper.We emphasize here that our proof of the simulation result applies only to the GPAC as described below. The GPAC's form a natural subclass of the class of all analog computers, and are based on certain idealized components (“black boxes”), mostly associated with the technology of past decades. One can easily envisage other kinds of black boxes of an input-output character that would lead to different kinds of analog computers. (For example, one could incorporate delays, or spatial integrators in addition to the present temporal integrators, etc.) Whether digital simulation is possible for these “extended” analog computers poses a rich and challenging set of research questions. (shrink)

The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The (...) stability and mobility of these solitons depended on the uniformity of dipole-dipole coupling between amide I oscillators, and the isotropy of the exciton-phonon interaction. Davydov solitons were also able to quantum tunnel through massive barriers, or to quantum interfere at collision sites. The results presented here support a nontrivial role of quantum effects in biological systems that lies beyond the mechanistic support of covalent bonds as binding agents of macromolecular structures. Quantum tunneling and interference of Davydov solitons provide catalytically active macromolecular protein complexes with a physical mechanism allowing highly efficient transport, delivery, and utilization of free energy, besides the evolutionary mandate of biological order that supports the existence of such genuine quantum phenomena, and may indeed demarcate the quantum boundaries of life. (shrink)

The numerically definite syllogistic is the fragment of English obtained by extending the language of the classical syllogism with numerical quantifiers. The numerically definite relational syllogistic is the fragment of English obtained by extending the numerically definite syllogistic with predicates involving transitive verbs. This paper investigates the computational complexity of the satisfiability problem for these fragments. We show that the satisfiability problem (= finite satisfiability problem) for the numerically definite syllogistic is strongly NP-complete, and that the satisfiability problem (= (...) finite satisfiability problem) for the numerically definite relational syllogistic is NEXPTIME-complete, but perhaps not strongly so. We discuss the related problem of probabilistic (propositional) satisfiability, and thereby demonstrate the incompleteness of some proof-systems that have been proposed for the numerically definite syllogistic. (shrink)

In the last 20 years, a stream of research emerged under the label of „complex problem solving“ (CPS). This research was intended to describe the way people deal with complex, dynamic, and intransparent situations. Complex computer-simulated scenarios were as stimulus material in psychological experiments. This line of research lead to subtle insights into the way how people deal with complexity and uncertainty. Besides these knowledge-rich, realistic, intransparent, complex, dynamic scenarios with many variables, a second line of (...) research used more simple, knowledge-lean scenarios with a low number of variables („minimal complex systems“, MCS) that have been proposed recently in problem-solving research for the purpose of educational assessment. In both cases, the idea behind the use of microworlds is to increase validity of problem solving tasks by presenting interactive environments that can be explored and controlled by participants while pursuing certain action goals. The main argument presented here is: both types of systems - CPS and MCS – can only be dealt with successfully if causal dependencies between input and output variables are identified and used for system control. System knowledge is necessary for control and intervention. But CPS and MCS differ in their way of how causal dependencies are identified and how the mental model is constructed; therefore, they cannot be compared directly to each other with respect to the cognitive processes that are necessary for solving the tasks. Knowledge-poor MCS tasks address only a small fraction of the cognitive processes and structures needed for knowledge-rich CPS situations. (shrink)

The ideas of quantum simulation and advances in quantum algorithms to solve quantum chemistry problems have been discussed. Theoretical proposals and experimental investigations both have been studied to gauge the extent to which quantum computation has been applied to solve quantum chemical problems till date. The distinctive features and limitations of the application of quantum simulation on chemical systems and current approaches to define and improve upon standard quantum algorithms have been (...) studied in detail. The possibility and consequences of designing an efficient quantum computer that can address chemical problems have been assessed. The experimental realization of quantum supremacy defies the conventional belief of chemists, that millions of qubits would be required to solve fundamental chemistry problems. It is predicted that quantum simulation of quantum chemistry problems will radically revolutionize this field. (shrink)

Shi and Aharonov have shown that the Toffoli gate and the Hadamard gate give rise to an approximately universal set of quantum computational gates. We study the basic algebraic properties of this system by introducing the notion of Shi-Aharonov quantum computational structure. We show that the quotient of this structure is isomorphic to a structure based on a particular set of complex numbers (the closed disc with center \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$(\frac{1}{2},\frac{1}{2})$\end{document} (...) and radius \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$\frac{1}{2}$\end{document} ). (shrink)

As brightly shown by Mainzer [24], the science of complexity has many distinct origins in many disciplines. Those various origins has led to “an interdisciplinary methodology to explain the emergence of certain macroscopic phenomena via the nonlinear interactions of microscopic elements” (ibid.). This paper suggests that the parallel and strong expansion of modeling and simulation - especially after the Second World War and the subsequent development of computers - is a rationale which also can be counted as an explanation (...) of this emergence. With the benefit of hindsight, one can find three periods in the methodologies of modeling in the empirical sciences: 1st the simple modeling of the simple, 2nd the simple modeling of the complex, 3rd the complex modeling and simulation of the complex. Our main thesis is that the current spreading (since the 90’s) of complex computer simulations of systems of models (where a simulation is no more a step by step calculus of a unique logico-mathematical model) is another promising dimension of the science of complexity. Following this claim, we propose to distinguish three different types of computer simulations in the context of complex systems’ modeling. Finally, we show that these types of simulations lead to three different types of weak emergence, too. (shrink)

Combining physics, mathematics and computer science, quantum computing and its sister discipline of quantum information have developed in the past few decades from visionary ideas to two of the most fascinating areas of quantum theory. General interest and excitement in quantum computing was initially triggered by Peter Shor (1994) who showed how a quantum algorithm could exponentially “speed-up” classical computation and factor large numbers into primes far more efficiently than any (known) classical algorithm. Shor’s (...) algorithm was soon followed by several other algorithms that aimed to solve combinatorial and algebraic problems, and in the years since theoretical study of quantum systems serving as computational devices has achieved tremendous progress. Common belief has it that the implementation of Shor’s algorithm on a large scale quantum computer would have devastating consequences for current cryptography protocols which rely on the premise that all known classical worst-case algorithms for factoring take time exponential in the length of their input (see, e.g., Preskill 2005). Consequently, experimentalists around the world are engaged in attempts to tackle the technological difficulties that prevent the realisation of a large scale quantum computer. But regardless whether these technological problems can be overcome (Unruh 1995; Ekert and Jozsa 1996; Haroche and Raimond 1996), it is noteworthy that no proof exists yet for the general superiority of quantum computers over their classical counterparts. -/- The philosophical interest in quantum computing is manifold. From a social-historical perspective, quantum computing is a domain where experimentalists find themselves ahead of their fellow theorists. Indeed, quantum mysteries such as entanglement and nonlocality were historically considered a philosophical quibble, until physicists discovered that these mysteries might be harnessed to devise new efficient algorithms. But while the technology for harnessing the power of 50–100 qubits (the basic unit of information in the quantum computer) is now within reach (Preskill 2018), only a handful of quantum algorithms exist, and the question of whether these can truly outperform any conceivable classical alternative is still open. From a more philosophical perspective, advances in quantum computing may yield foundational benefits. For example, it may turn out that the technological capabilities that allow us to isolate quantum systems by shielding them from the effects of decoherence for a period of time long enough to manipulate them will also allow us to make progress in some fundamental problems in the foundations of quantum theory itself. Indeed, the development and the implementation of efficient quantum algorithms may help us understand better the border between classical and quantum physics (Cuffaro 2017, 2018a; cf. Pitowsky 1994, 100), and perhaps even illuminate fundamental concepts such as measurement and causality. Finally, the idea that abstract mathematical concepts such as computability and complexity may not only be translated into physics, but also re-written by physics bears directly on the autonomous character of computer science and the status of its theoretical entities—the so-called “computational kinds”. As such it is also relevant to the long-standing philosophical debate on the relationship between mathematics and the physical world. (shrink)

Viewed in the light of the remarkable performance of ‘Watson’ - IBMs proprietary artificial intelligence computer system capable of answering questions posed in natural language - on the US general knowledge quiz show ‘Jeopardy’, we review two experiments on formal systems - one in the domain of quantum physics, the other involving a pictographic languaging game - whereby behaviour seemingly characteristic of domain understanding is generated by the mere mechanical application of simple rules. By re-examining both experiments in (...) the context of Searle’s Chinese Room Argument, we suggest their results merely endorse Searle’s core intuition: that ‘syntactical manipulation of symbols is not sufficient for semantics’. Although, pace Watson, some artificial intelligence practitioners have suggested that more complex, higher-level operations on formal symbols are required to instantiate understanding in computational systems, we show that even high-level calls to Google translate would not enable a computer qua ‘formal symbol processor’ to understand the language it processes. We thus conclude that even the most recent developments in ‘quantum linguistics’ will not enable computational systems to genuinely understand natural language. (shrink)

This paper considers the potential impact that the nascent technology of quantum computing may have on society. It focuses on three areas: cryptography, optimization, and simulation of quantum systems. We will also discuss some ethical aspects of these developments, and ways to mitigate the risks.

1. The Physical Church-Turing Thesis. Physicists often interpret the Church-Turing Thesis as saying something about the scope and limitations of physical computing machines. Although this was not the intention of Church or Turing, the Physical Church Turing thesis is interesting in its own right. Consider, for example, Wolfram’s formulation: One can expect in fact that universal computers are as powerful in their computational capabilities as any physically realizable system can be, that they can simulate any physical system . . (...) . No physically implementable procedure could then shortcut a computationally irreducible process. (Wolfram 1985) Wolfram’s thesis consists of two parts: (a) Any physical system can be simulated (to any degree of approximation) by a universal Turing machine (b) Complexity bounds on Turing machine simulations have physical significance. For example, suppose that the computation of the minimum energy of some system of n particles takes at least exponentially (in n) many steps. Then the relaxation time of the actual physical system to its minimum energy state will also take exponential time. (shrink)

In this paper, we investigate the numerical solution of the coupled fractional massive Thirring equation with the aid of He’s fractional complex transform. This study plays a significant aspect in the field of quantum physics, weakly nonlinear thrilling waves, and nonlinear optics. The main advantage of FCT is that it converts the fractional differential equation into its traditional parts and is also capable to handle the fractional order, whereas the homotopy perturbation method is employed to tackle the (...) nonlinear terms in the coupled fractional massive Thirring equation. An example is illustrated to present the efficiency and validity of the two-scale theory. The solutions are obtained in the form of series with simple and easy computations which confirm that the present approach is good in agreement and is easy to implement for such type of complex systems in science and engineering. (shrink)

This article presents two approaches for computer simulations of virtue ethics in the context of agent-based modeling, a simple way and a complex way. The simple way represents virtues as numeric variables that are invoked in specific events or situations. This way can easily be implemented and included in social simulations. On the other hand, the complex way requires a PECS framework: physical, cognitive, emotional, and social components need to be implemented in agents. Virtue is the (...) result of the interaction of these internal components rather than a single variable. I argue that the complex way using the PECS framework is more suitable for simulating virtue ethics theory because it can capture the internal struggle and conflict sometimes involved in the practice of virtue. To show how the complex way could function, I present a sample computer simulation for the cardinal virtue of temperance, the virtue that moderates physical desires such as food, drink, and sex. This computer simulation is programmed in Python and builds upon the well-known Sugarscape simulation.1. (shrink)

The theory of nonlinear complex systems has become a successful and widely used problem-solving approach in the natural sciences - from laser physics, quantum chaos and meteorology to molecular modeling in chemistry and computer simulations of cell growth in biology. In recent times it has been recognized that many of the social, ecological and political problems of mankind are also of a global, complex and nonlinear nature. And one of the most exciting topics of present (...) scientific and public interest is the idea that even the human mind is governed largely by the nonlinear dynamics of complex systems. In this wide-ranging but concise treatment Prof. Mainzer discusses, in nontechnical language, the common framework behind these endeavours. Special emphasis is given to the evolution of new structures in natural and cultural systems and it is seen clearly how the new integrative approach of complexity theory can give new insights that were not available using traditional reductionistic methods. (shrink)

Systems of logico-probabilistic reasoning characterize inference from conditional assertions that express high conditional probabilities. In this paper we investigate four prominent LP systems, the systems _O, P_, _Z_, and _QC_. These systems differ in the number of inferences they licence _. LP systems that license more inferences enjoy the possible reward of deriving more true and informative conclusions, but with this possible reward comes the risk of drawing more false or uninformative conclusions. In the first (...) part of the paper, we present the four systems and extend each of them by theorems that allow one to compute almost-tight lower-probability-bounds for the conclusion of an inference, given lower-probability-bounds for its premises. In the second part of the paper, we investigate by means of computer simulations which of the four systems provides the best balance of reward versus risk. Our results suggest that system _Z_ offers the best balance. (shrink)

Tissue P systems with evolutional communication rules are computational models inspired by biochemical systems consisting of multiple individuals living and cooperating in a certain environment, where objects can be modified when moving from one region to another region. In this work, cell separation, inspired from membrane fission process, is introduced in the framework of tissue P systems with evolutional communication rules. The computational complexity of this kind of P systems is investigated. It is proved that only (...) problems in class P can be efficiently solved by tissue P systems with cell separation with evolutional communication rules of length at most, for each natural number n≥1. In the case where that length is upper bounded by, a polynomial time solution to the SAT problem is provided, hence, assuming that P≠NP a new boundary between tractability and NP-hardness on the basis of the length of evolutional communication rules is provided. Finally, a new simulator for tissue P systems with evolutional communication rules is designed and is used to check the correctness of the solution to the SAT problem. (shrink)

The computational view of mind rests on certain intuitions regarding the fundamental similarity between computation and cognition. We examine some of these intuitions and suggest that they derive from the fact that computers and human organisms are both physical systems whose behavior is correctly described as being governed by rules acting on symbolic representations. Some of the implications of this view are discussed. It is suggested that a fundamental hypothesis of this approach is that there is (...) a natural domain of human functioning that can be addressed exclusively in terms of a formal symbolic or algorithmic vocabulary or level of analysis. Much of the paper elaborates various conditions that need to be met if a literal view of mental activity as computation is to serve as the basis for explanatory theories. The coherence of such a view depends on there being a principled distinction between functions whose explanation requires that we posit internal representations and those that we can appropriately describe as merely instantiating causal physical or biological laws. In this paper the distinction is empirically grounded in a methodological criterion called the " cognitive impenetrability condition." Functions are said to be cognitively impenetrable if they cannot be influenced by such purely cognitive factors as goals, beliefs, inferences, tacit knowledge, and so on. Such a criterion makes it possible to empirically separate the fixed capacities of mind from the particular representations and algorithms used on specific occasions. In order for computational theories to avoid being ad hoc, they must deal effectively with the "degrees of freedom" problem by constraining the extent to which they can be arbitrarily adjusted post hoc to fit some particular set of observations. This in turn requires that the fixed architectural function and the algorithms be independently validated. It is argued that the architectural assumptions implicit in many contemporary models run afoul of the cognitive impenetrability condition, since the required fixed functions are demonstrably sensitive to tacit knowledge and goals. The paper concludes with some tactical suggestions for the development of computational cognitive theories. (shrink)

Massively multiplayer online games are not merely electronic communication systems based on computational databases, but also include artificial intelligence that possesses complex, dynamic structure. Each visible action taken by a component of the multi-agent system appears simple, but is supported by vastly more sophisticated invisible processes. A rough outline of the typical hierarchy has four levels: interaction between two individuals, each either human or artificial, conflict between teams of agents who cooperate with fellow team members, enduring social-cultural groups (...) that seek to accomplish shared goals, and large-scale cultural traditions, often separated into virtual geographic regions. In many MMOs, both magic and religion are represented, in ways that harmonize with a social-scientific theory that defines them in terms of specific versus general psychological compensators. This article draws empirical examples from five diverse MMOs: Dark Age of Camelot, Dungeons and Dragons Online, World of Warcraft, A Tale in the Desert and Gods and Heroes. (shrink)

This book is designed to make accessible to nonspecialists the still evolving concepts of quantum mechanics and the terminology in which these are expressed. The opening chapters summarize elementary concepts of twentieth century quantum mechanics and describe the mathematical methods employed in the field, with clear explanation of, for example, Hilbert space, complex variables, complex vector spaces and Dirac notation, and the Heisenberg uncertainty principle. After detailed discussion of the Schrödinger equation, subsequent chapters focus on isotropic (...) vectors, used to construct spinors, and on conceptual problems associated with measurement, superposition, and decoherence in quantum systems. Here, due attention is paid to Bell's inequality and the possible existence of hidden variables. Finally, progression toward quantum computation is examined in detail: if quantum computers can be made practicable, enormous enhancements in computing power, artificial intelligence, and secure communication will result. This book will be of interest to a wide readership seeking to understand modern quantum mechanics and its potential applications. (shrink)

In silico medicine is still forging a road for itself in the current biomedical landscape. Discursively and rhetorically, it is using a three-way positioning, first, deploying discourses of personalised medicine, second, extending the 3Rs from animal to clinical research, and third, aligning its methods with experimental methods. The discursive and rhetorical positioning in promotions and statements of the programme gives us insight into the sociability of the scientific labour of advancing the programme. Its progress depends on complex social, institutional (...) and technological conditions which are not external to its epistemology, but intricately interwoven with it. This article sets out to show that this is the case through an analysis of the process of computational modelling that is at the core of its epistemology. In this paper I show that the very notion of ‘model’ needs to be re-thought for in silico medicine, and propose a replacement, in the form of the ‘Model-Simulation-Experiment-System’ or MSE-system, which is simultaneously an epistemological, social and technological system. I argue that the MSE-system is radically mediated by social relations, technologies and symbolic systems. We need now to understand how such mediations operate effectively in the construction of robust MSE-systems. (shrink)

Regarding the continuous development of high-speed trains and the increase of running speeds, the aerodynamic design of high-speed trains has become significantly important, while reduction of drag and noise comprises a significant challenge in order to optimize aerodynamic design of high-speed trains. The design form factor of a high-speed train is highly influenced by aerodynamic aspects including aerodynamic drag, lift force, and noise. With the high-speed train as the object, the paper aims to take bionic concept as the entry point, (...) selecting the hummingbird as the bionic prototype and extracting bionic elements to establish a bionic train model. Then, the finite volume method was used for numerical simulation and analysis of the aerodynamic performance and aerodynamic noise of the bionic high-speed train. Computational results prove that drag and noise of the bionic head type were lower than those of the original train; drag of the head train of the bionic model was reduced by 2.21% in comparison with the original model, while the whole-train drag was reduced by 3.53%, indicating that drag reduction effects are available and implying that the bionic head type could reduce drag and noise. Noise sources of the bionic train are mainly located at positions with easy airflow separation and violent turbulence motion. Large turbulence energy is in bogie areas and mainly exists at the leeward side of the bogie area. Obviously, the bogie area is the major noise source of the train. Aerodynamic noise of the bionic train in far-field comprises a wide-frequency range. Noises were concentrated within 613 Hz~3150 Hz. When the bionic high-speed train ran at 350 km/h, through comparative analysis of total noise levels at observed points of the high-speed train, it is found that this position with the maximum noise level was 25 m away from the head train nose tip, with the maximum value of 88.4 dB. When the bionic train ran at 600 km/h, the maximum sound pressure level at the longitudinal point was 99.7 dB and the average noise level was 96.6 dB. When the running speed increased from 350 km/h to 600 km/h, the maximum noise level increased by 11.3 dB and the average noise level increased by 11.6 dB. Computation results of aerodynamic noise at the point which is 7.5 m away from the rail center show that the maximum aerodynamic noise level existed at the first-end bogie of the head train, while the noise level was larger at the position closer to the ground. (shrink)

Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation (...) and other tools to handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations. (shrink)

Based on the existing financial system risk models, a set of time-lag financial system risk models is established considering the influence brought by time-lag factors on the financial risk system, and the dynamical behavior of this system is analyzed by using chaos theory. Through Matlab simulation, the bifurcation diagram and phase diagram of time-lag risk intensity and control intensity are plotted. The analysis shows that this kind of time-lag financial system risk model has complex dynamic behavior, different motion states (...) will appear when different parameter values are selected, and the time-lag risk intensity parameter also has a very strong influence on the system motion. To ensure the operation of the financial system in a stable state, measures with certain delay effects must be taken to control the risk and to choose the appropriate time-lag control intensity, and too much or too little time-lag control intensity is not conducive to the benign operation of the system. (shrink)

The present paper introduces "ontomimetic simulation" and argues that this class of models has enabled the investigation of hypotheses about complex systems in new ways that have epistemological relevance. Ontomimetic simulation can be differentiated from other types of modeling by its reliance on causal similarity in addition to representation. Phenomena are modeled not directly but via mimesis of the ontology (i.e. the "underlying physics", microlevel etc.) of systems and a subsequent animation of the resulting model ontology as (...) a dynamical system. While the ontology is clearly used for computing system states, what is epistemologically important is that it is viewed as a hypothesis about the makeup of the studied system. This type of simulation, where model ontologies are used as hypotheses, is here called inverse ontomimetic simulation since it reverses the typical informational path from the target to the model system. It links experimental and analytical techniques in being explicitly dynamical while at the same time capable of abstraction. Inverse ontomimetic simulation is argued to have a great impact on science and to be the tool for hypothesis-testing that has made systematic theory development for complex systems possible. (shrink)

Until the late 19th century scientists almost always assumed that the world could be described as a rule-based and hence deterministic system or as a set of such systems. The assumption is maintained in many 20th century theories although it has also been doubted because of the breakthrough of statistical theories in thermodynamics (Boltzmann and Gibbs) and other fields, unsolved questions in quantum mechanics as well as several theories forwarded within the social sciences. Until recently it has furthermore (...) been assumed that a rule-based and deterministic system was also predictable if only the rules were known, but this assumption has now been undermined by modern chaos-theory describing rule-based and deterministic, but unpredictable systems, while catastrophe-theory delivers a set of types describing various kinds of instability and conditions for the stability of a given system. Hence the main trait in the theoretical development in the 20th-century science can be described as a basic modification and limitation of some of the fundamental and strong assumptions forwarded in the previous epochs of modern science. Ironically, the very same process has been a process in which the human capacity to intervene in nature has expanded dramatically and mainly with the help of the very same theories, and not least because they allow nature to be described and made manipulable on a lower level and a more fine-grained scale. While the overall theoretical consistency between the various theories has gone, the reach of human intervention in nature has increased based on quite new dimensions whether in the area of physics (e.g.: energy technologies, chemical technologies, nanotechnologies etc.) or biology (ge¬netic manipulation) or in the area of psychology, sociology and culture (artificial simulations of mental processes, new means of communication, implying changes in the social infrastructure and cultural behaviour etc.). While some of these changes and new conditions can be reflected from within the conceptual framework of rule-based systems, albeit more complex than formerly recognized, others seem to give rise to the question of whether there are »systems« and relations between different systems in the world which are not rule-based? For instance, it seems to be obvious that the notion of instability represents a major conceptual break with former theories of rule-based systems, as the stability of the latter is an axiomatically given property implied in the very notion of rule-based systems, while instability can only be the result of external influence which should be explained as the result of another rule-based sy¬stem. While there are no difficulties implied concerning the stability of rule-based systems, the notion of unstable states of a system raises the question of how there can be a system at all if there are no invariant stabilising principles? This is the first question which I will address. And I shall do so by taking two examples of such systems as my point of departure. The first example will be the computer and the second will be ordinary language. In both cases I will argue that the stability of these systems (which are both defined by the existence/presence of human intentions) are provided by the help of - differently organised - redundancy functions which both allow the maintenance of systems in unstable macro-states, suspension of previous rules, underdetermination and overdetermination and generation/emergence/creation of new rules more or less independent of previous rules by the help of optional recursions to the permanently accessible underlying levels as for instance the level of binary representation in computers. Since the notion of redundancy is both controversial as such and often avoided, the concept is discussed (as defined in Claude Shannon's mathematical theory of information and in the semiotic framework of J. J. Greimas) and leading to a more general definition in which the redundancy functions serve to overcome noisy conditions, but at the cost of rule-based stability, determination, and predictability. A second question will be how the notion of rule-generating systems relates to the notion of anticipatory systems and it will be argued that rule-generating systems share some features with an¬ticipatory systems and that the former from a certain viewpoint can be seen as a subclass of the latter, although anticipative features are not necessarily a part of the definition of rule-generating systems. On the other hand, it will be discussed whether anticipatory systems which are not rule-generating systems can exist and it will be argued that the capacity to anticipate is strongly limited if it is not part of a rule-generating system. Therefore, it is concluded that the most powerful anticipatory systems need to be rule-generating systems. (shrink)

Computational complexity theory is a branch of computer science dedicated to classifying computational problems in terms of their difficulty. While computability theory tells us what we can compute in principle, complexity theory informs us regarding our practical limits. In this chapter I argue that the science of \emph{quantum computing} illuminates complexity theory by emphasising that its fundamental concepts are not model-independent, but that this does not, as some suggest, force us to radically revise the foundations of the theory. For (...) model-independence never has been essential to those foundations. The fundamental aim of complexity theory is to describe what is achievable in practice under various models of computation for our various practical purposes. Reflecting on quantum computing illuminates complexity theory by reminding us of this, too often under-emphasised, fact. (shrink)

Now that complex Agent-Based Models and computer simulations spread over economics and social sciences - as in most sciences of complex systems -, epistemological puzzles (re)emerge. We introduce new epistemological concepts so as to show to what extent authors are right when they focus on some empirical, instrumental or conceptual significance of their model or simulation. By distinguishing between models and simulations, between types of models, between types of computer simulations and between types of (...) empiricity obtained through a simulation, section 2 gives the possibility to understand more precisely - and then to justify - the diversity of the epistemological positions presented in section 1. Our final claim is that careful attention to the multiplicity of the denotational powers of symbols at stake in complex models and computer simulations is necessary to determine, in each case, their proper epistemic status and credibility. (shrink)

This paper examines several issues related to information, speed of computation, and simulation of a physical process. It is argued that mental processes proceed at a rate close to the optimal based on thermodynamic considerations. Problems related to the simulation of a quantum mechanical system on a computer are reviewed. Parallels are drawn between biological and adaptive quantum systems.

Critical in the computationalist account of the mind is the phenomenon called computational or computer simulation of human thinking, which is used to establish the theses that human thinking is a computational process and that computing machines are thinking systems. Accordingly, if human thinking can be simulated computationally then human thinking is a computational process; and if human thinking is a computational process then its computational simulation is itself a thinking process. This paper shows that the said phenomenon—the computational (...) simulation of human thinking—is ill-conceived, and that, as a consequence, the theses that it intends to establish are problematic. It is argued that what is simulated computationally is not human thinking as such but merely its behavioral manifestations; and that a computational simulation of these behavioral manifestations does not necessarily establish that human thinking is computational, as it is logically possible for a non-computational system to exhibit behaviors that lend themselves to a computational simulation. (shrink)

This textbook carefully develops the main ideas and techniques of statistical and thermal physics and is intended for upper-level undergraduate courses. The authors each have more than thirty years' experience in teaching, curriculum development, and research in statistical and computational physics. Statistical and Thermal Physics begins with a qualitative discussion of the relation between the macroscopic and microscopic worlds and incorporates computer simulations throughout the book to provide concrete examples of important conceptual ideas. Unlike many contemporary texts on thermal (...) physics, this book presents thermodynamic reasoning as an independent way of thinking about macroscopic systems. Probability concepts and techniques are introduced, including topics that are useful for understanding how probability and statistics are used. Magnetism and the Ising model are considered in greater depth than in most undergraduate texts, and ideal quantum gases are treated within a uniform framework. Advanced chapters on fluids and critical phenomena are appropriate for motivated undergraduates and beginning graduate students. Integrates Monte Carlo and molecular dynamics simulations as well as other numerical techniques throughout the text Provides self-contained introductions to thermodynamics and statistical mechanics Discusses probability concepts and methods in detail Contains ideas and methods from contemporary research Includes advanced chapters that provide a natural bridge to graduate study Features more than 400 problems Programs are open source and available in an executable cross-platform format Solutions manual. (shrink)

Scientists depend on complex computational systems that are often ineliminably opaque, to the detriment of our ability to give scientific explanations and detect artifacts. Some philosophers have s...

Open peer commentary on the article “Info-computational Constructivism and Cognition” by Gordana Dodig-Crnkovic. Upshot: Dodig-Crnkovic’s “info-computational constructivism” (IC), as an essential part of a constructivist approach, needs integration with the logical, mathematical and physical evidence coming from quantum field theory (QFT) as the fundamental physics of the emergence of “complex systems” in all realms of natural sciences.

The distinction at the heart of van Gelder’s target article is one between digital computers and dynamical systems. But this distinction conflates two more fundamental distinctions in cognitive science that should be keep apart. When this conflation is undone, it becomes apparent that the “computational hypothesis” (CH) is not as dominant in contemporary cognitive science as van Gelder contends; nor has the “dynamical hypothesis” (DH) been neglected.

This article explores some of the roles of computer simulation in measurement. A model-based view of measurement is adopted and three types of measurement—direct, derived, and complex—are distinguished. It is argued that while computer simulations on their own are not measurement processes, in principle they can be embedded in direct, derived, and complex measurement practices in such a way that simulation results constitute measurement outcomes. Atmospheric data assimilation is then considered as a case study. This practice, which (...) involves combining information from conventional observations and simulation-based forecasts, is characterized as a complex measuring practice that is still under development. The case study reveals challenges that are likely to resurface in other measuring practices that embed computer simulation. It is also noted that some practices that embed simulation are difficult to classify; they suggest a fuzzy boundary between measurement and non-measurement. 1 Introduction2 A Contemporary View of Measurement3 Three Types of Measurement4 Can Computer Simulations Measure Real-World Target Systems?5 Case Study: Atmospheric Data Assimilation5.1 Why data assimilation?5.2 A complex measuring practice under development5.3 Epistemic iteration6 The Boundaries of Measurement7 Epistemology, Not Terminology. (shrink)

Now that complex Agent-Based Models and computer simulations spread over economics and social sciences - as in most sciences of complex systems -, epistemological puzzles (re)emerge. We introduce new epistemological tools so as to show to what precise extent each author is right when he focuses on some empirical, instrumental or conceptual significance of his model or simulation. By distinguishing between models and simulations, between types of models, between types of computer simulations and between (...) types of empiricity, section 2 gives conceptual tools to explain the rationale of the diverse epistemological positions presented in section 1. Finally, we claim that a careful attention to the real multiplicity of denotational powers of symbols at stake and then to the implicit routes of references operated by models and computer simulations is necessary to determine, in each case, the proper epistemic status and credibility of a given model and/or simulation. (shrink)

We show that there is a structure of countably infinite signature with $P = N_{2}P$ and a structure of finite signature with $P = N_{1}P$ and $N_{1}P \neq N_{2}P$ . We give a further example of a structure of finite signature with $P \neq N_{1}P$ and $N_{1}P \neq N_{2}P$ . Together with a result from [10] this implies that for each possibility of P versus NP over structures there is an example of countably infinite signature. Then we show that (...) for some finite ℒ the class of ℒ-structures with $P = N_{1}P$ is not closed under ultraproducts and obtain as corollaries that this class is not $\delta$ -elementary and that the class of ᵍ-structures with $P \neq N_{1}P$ is not elementary. Finally we prove that for all f dominating all polynomials there is a structure of finite signature with the following properties: $P \neq N_{1}P$ . $N_{1}P \neq N_{2}P$ , the levels $N_{2}TIME(n^{i})$ of $N_{2}P$ and the levels $N_{1}TIME(n^{i})$ of $N_{1}P$ are different for different i, indeed $DTIME(n^{i'}) \nsubseteq N_{2}TIME(n^{i})$ if $i' \textgreater i$ ; $DTIME(f) \nsubseteq N_{2}P$ , and $N_{2}P \nsubseteq DEC$ . DEC is the class of recognizable sets with recognizable complements. So this is an example where the internal structure of $N_{2}P$ is analyzed in a more detailed way. In our proofs we use methods in the style of classical computability theory to construct structures except for one use of ultraproducts. (shrink)

I discuss here the definition of computer simulations, and more specifically the views of Humphreys, who considers that an object is simulated when a computer provides a solution to a computational model, which in turn represents the object of interest. I argue that Humphreys's concepts are not able to analyse fully successfully a case of contemporary simulation in physics, which is more complex than the examples considered so far in the philosophical literature. I therefore modify Humphreys's definition of (...) simulation. I allow for several successive layers of computational models, and I discuss the relations that exist between these models, the computer, and the object under study. An aim of my proposal is to clarify the distinction between computational models and numerical methods, and to better understand the representational and the computational functions of models in simulations. (shrink)

Verification and validation of computer codes and models used in simulations are two aspects of the scientific practice of high importance that recently have been discussed widely by philosophers of science. While verification is predominantly associated with the correctness of the way a model is represented by a computer code or algorithm, validation more often refers to the model’s relation to the real world and its intended use. Because complex simulations are generally opaque to a practitioner, the (...) Duhem problem can arise with verification and validation due to their entanglement; such an entanglement makes it impossible to distinguish whether a coding error or the model’s general inadequacy to its target should be blamed in the case of a failure. I argue that a clear distinction between computer modeling and simulation has to be made to disentangle verification and validation. Drawing on that distinction, I suggest to associate modeling with verification and simulation, which shares common epistemic strategies with experimentation, with validation. To explain the reasons for their entanglement in practice, I propose a Weberian ideal–typical model of modeling and simulation as roles in practice. I examine an approach to mitigate the Duhem problem for verification and validation that is generally applicable in practice and is based on differences in epistemic strategies and scopes. Based on this analysis, I suggest two strategies to increase the reliability of simulation results, namely, avoiding alterations of verified models at the validation stage as well as performing simulations of the same target system using two or more different models. In response to Winsberg’s claim that verification and validation are entangled I argue that deploying the methodology proposed in this work it is possible to mitigate inseparability of V&V in many if not all domains where modeling and simulation are used. (shrink)

In this Short Communication we will discuss the role played by quantum computing within the emerging morphological paradigm in the unconventional natural computing. We intend merely introduce the main reasons why a coherent representation of Universality in morphological natural computing needs to be grounded on a version of Quantum Field Theory independent, in many senses, from the Quantum Mechanics formalism in fundamental physics, namely formulated as a thermal field theory. This theory describes the “emergence” of natural information (...) and computation’s complexity at a quantum level, thus overcoming the trivializing argument against the so-called “pancomputationalism” in morphological natural computing. (shrink)

Proposed models of closed timelike curves have been shown to enable powerful information-processing protocols. We examine the simulation of models of CTCs both by other models of CTCs and by physical systems without access to CTCs. We prove that the recently proposed transition probability CTCs are physically equivalent to postselection CTCs, in the sense that one model can simulate the other with reasonable overhead. As a consequence, their information-processing capabilities are equivalent. We also describe a method for quantum (...) computers to simulate Deutschian CTCs. In cases for which the overhead is reasonable, it might be possible to perform the simulation in a table-top experiment. This approach has the benefit of resolving some ambiguities associated with the equivalent circuit model of Ralph et al. Furthermore, we provide an explicit form for the state of the CTC system such that it is a maximum-entropy state, as prescribed by Deutsch. (shrink)