Application of molecular dynamics computer simulations in the design of a minimal self‐replicating molecular machine

It is commonly agreed that a chemical assembly of molecules can be considered alive if it can ingest resources and convert them into building blocks; has the ability to grow and self‐reproduce; and can evolve. In the design proposed by Rasmussen and Chen (Science 2004, 303, 963) the assembly or protocell could be as simple as a small micellar surfactant aggregate acting as a container, anchoring an informational molecule to its exterior and incorporating a metabolism within the oily interior. We present several examples of modeling such a system with molecular dynamics computer simulations. © 2008 Wiley Periodicals, Inc. Complexity, 2008.     

Confined steady states of a Vlasov‐Poisson plasma in an infinitely long cylinder

We consider the two‐dimensional Vlasov‐Poisson system to model a two‐component plasma whose distribution function is constant with respect to the third space dimension. First, we show how this two‐dimensional Vlasov‐Poisson system can be derived from the full three‐dimensional model. The existence of compactly supported steady states with vanishing electric potential in a three‐dimensional setting has already been investigated in the literature. We show that these results can easily be adapted to the two‐dimensional system. However, our main result is to prove the existence of compactly supported steady states even with a nontrivial self‐consistent electric potential.     

Contextual regularity and complexity of neuronal activity: From stand‐alone cultures to task‐performing animals

Precursors of the superior information processing capabilities of our cortex can most probably be traced back to simple invertebrate systems. Using a unique set of newly developed neuronal preparations and state‐of‐the‐art analysis tools, we show that insect neurons have the ability to self‐regulate the information capacity of their electrical activity. We characterize the activity of a distinct population of neurons under progressive levels of structural and functional constraints: self‐formed networks of neuron clusters in vitro; isolated ex vivo ganglions; in vivo task‐free, and in vivotask‐forced neuronal activity in the intact animal. We show common motifs and identify trends of increasing self‐regulated complexity. This important principle may have played a key role in the gradual transition from simple neuronal motor control to complex information processing. © 2004 Wiley Periodicals, Inc. Complexity 9: 25–32, 2004     

Life‐like self‐reproducers

In order to understand the interplay among information, genetic instructions, and phenotypic variations, self‐reproducers discovered in two‐dimensional cellular automata are considered as proto‐organisms, which undergo to mutations as they were in a real environmental situation. We realized a computational model through which we have been able to discover the genetic map of the self‐reproducers and the networks they use. Identifying in these maps sets of different functional genes, we found that mutations in the genetic sequences could affect both external shapes and behavior of the self‐reproducers, thus realizing different life‐like strategies in the evolution process. The results highlight that some strategies evolution uses in selecting organisms that are fitting with changing environmental situations maintain the self‐reproducing function, whereas other variations create new self‐reproducers. These self‐reproducers in turn realize different genetic networks, which can be very different from the basic ancestors pools. The mutations that are disruptive bring self‐reproducers to disappear, while other proto‐organisms are generated. © 2004 Wiley Periodicals, Inc. Complexity 9: 38–55, 2004     

On the complexity of finding paths in a two‐dimensional domain I: Shortest paths

The computational complexity of finding a shortest path in a two‐dimensional domain is studied in the Turing machine‐based computational model and in the discrete complexity theory. This problem is studied with respect to two formulations of polynomial‐time computable two‐dimensional domains: (A) domains with polynomialtime computable boundaries, and (B) polynomial‐time recognizable domains with polynomial‐time computable distance functions. It is proved that the shortest path problem has the polynomial‐space upper bound for domains of both type (A) and type (B); and it has a polynomial‐space lower bound for the domains of type (B), and has a #P lower bound for the domains of type (A). (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Minimizing transient times in a coupled solid‐state laser model

We consider a system of ordinary differential equations modelling the dynamics of two coupled solid‐state lasers. Under the dynamics, this system may execute transitions between in‐phase and out‐of‐phase states. For satellite communications and high‐speed data transfer the transition times should be reduced to their shortest possible duration. In this paper, we apply optimal control theory to find the values of various laser parameters (e.g. the amplitude of the injected field, detunings, and coupling constants) which minimize the transient times between out‐of‐phase and in‐phase states. The effect of each parameter is shown to be independent of the other two, and the transient time is shown to be a strictly increasing function of detuning and a strictly decreasing function of the coupling constant and amplitude of the injected field. The effect of initial conditions on transient times is also analysed. Published in 2005 by John Wiley & Sons, Ltd.     

Complex genetic evolution of artificial self‐replicators in cellular automata

It is widely believed that evolutionary dynamics of artificial self‐replicators realized in cellular automata (CA) are limited in diversity and adaptation. Contrary to this view, we show that complex genetic evolution may occur within simple CA. The evolving self‐replicating loops (“evoloops”) we investigate exhibit significant diversity in macro‐scale morphologies and mutational biases, undergoing nontrivial genetic adaptation by maximizing colony density and enhancing sustainability against other species. Nonmutable subsequences enable genetic operations that alter fitness differentials and promote long‐term evolutionary exploration. These results demonstrate a unique example of genetic evolution hierarchically emerging from local interactions between elements much smaller than individual replicators. © 2004 Wiley Periodicals, Inc. Complexity 10: 33–39, 2004     

Complex dynamics of a discrete fractional‐order Leslie‐Gower predator‐prey model

A proposed discretized form of fractional‐order prey‐predator model is investigated. A sufficient condition for the solution of the discrete system to exist and to be unique is determined. Jury stability test is applied for studying stability of equilibrium points of the discretized system. Then, the effects of varying fractional order and other parameters of the systems on its dynamics are examined. The system undergoes Neimark‐Sacker and flip bifurcation under certain conditions. We observe that the model exhibits chaotic dynamics following stable states as the memory parameter α decreases and step size h increases. Theoretical results illustrate the rich dynamics and complexity of the model. Numerical simulation validates theoretical results and demonstrates the presence of rich dynamical behaviors include S‐asymptotically bounded periodic orbits, quasi‐periodicity, and chaos. The system exhibits a wide range of dynamical behaviors for fractional‐order α key parameter.     

Evolution in complex systems

What features characterize complex system dynamics? Power laws and scale invariance of fluctuations are often taken as the hallmarks of complexity, drawing on analogies with equilibrium critical phenomena. Here we argue that slow, directed dynamics, during which the system's properties change significantly, is fundamental. The underlying dynamics is related to a slow, decelerating but spasmodic release of an intrinsic strain or tension. Time series of a number of appropriate observables can be analyzed to confirm this effect. The strain arises from local frustration. As the strain is released through “quakes,” some system variable undergoes record statistics with accompanying log‐Poisson statistics for the quake event times. We demonstrate these phenomena via two very different systems: a model of magnetic relaxation in type II superconductors and the Tangled Nature model of evolutionary ecology and show how quantitative indications of aging can be found. © 2004 Wiley Periodicals, Inc. Complexity 10: 49–56, 2004     

On Dimensional Adaptivity For Mixed Beam‐Shell‐Structures

A hierarchical model for dimensional adaptivity, using mixed beam‐shell structures, is presented. Thin‐walled beam structures are often calculated on the base of beam theories. Parts of the global structure, like framework corners, are usually analyzed with shell elements in a separate model. To minimize the modeling and calculation expense, a transition element to couple beam and shell structures is used. A dimensional adaptiv algorithm is introduced to automate this the procedure of modeling and calculation. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

On a Model for Fires in Tunnel Network Structures

A one dimensional model to describe the dynamics of tunnelfires is used to model tunnel network structures. The corresponding conditions at the nodes are formulated. A numerical methods is presented. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Experiments on baroclinic instabilities

We study experiments on baroclinic instabilities in a different heated rotating annulus cooled from within. Characteristic time series of the flow velocity are measured with the Laser–Doppler–Velocimetry (LDV) technique. The surface flow is observed with a co–rotating camera. Steady waves as well as complex flow states are observed. Hysteresis is also found. The drift rate of stable baroclinic waves is determined. The methods of non–linear time series analysis are used to investigate the dynamics of baroclinic waves, particulary in transition zones between different flow regimes. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Densely defined non‐closable curl on carpet‐like metric measure spaces

The paper deals with the possibly degenerate behaviour of the exterior derivative operator defined on 1‐forms on metric measure spaces. The main examples we consider are the non self‐similar Sierpinski carpets recently introduced by Mackay, Tyson and Wildrick. Although topologically one‐dimensional, they may have positive two‐dimensional Lebesgue measure and carry nontrivial 2‐forms. We prove that in this case the curl operator (and therefore also the exterior derivative on 1‐forms) is not closable, and that its adjoint operator has a trivial domain. We also formulate a similar more abstract result. It states that for spaces that are, in a certain way, structurally similar to Sierpinski carpets, the exterior derivative operator taking 1‐forms into 2‐forms cannot be closable if the martingale dimension is larger than one.     

Using self‐dissimilarity to quantify complexity

For many systems characterized as “complex” the patterns exhibited on different scales differ markedly from one another. For example, the biomass distribution in a human body “looks very different” depending on the scale at which one examines it. Conversely, the patterns at different scales in “simple” systems (e.g., gases, mountains, crystals) vary little from one scale to another. Accordingly, the degrees of self‐dissimilarity between the patterns of a system at various scales constitute a complexity “signature” of that system. Here we present a novel quantification of self‐dissimilarity. This signature can, if desired, incorporate a novel information‐theoretic measure of the distance between probability distributions that we derive here. Whatever distance measure is chosen, our quantification of self‐dissimilarity can be measured for many kinds of real‐world data. This allows comparisons of the complexity signatures of wholly different kinds of systems (e.g., systems involving information density in a digital computer vs. species densities in a rain forest vs. capital density in an economy, etc.). Moreover, in contrast to many other suggested complexity measures, evaluating the self‐dissimilarity of a system does not require one to already have a model of the system. These facts may allow self‐dissimilarity signatures to be used as the underlying observational variables of an eventual overarching theory relating all complex systems. To illustrate self‐dissimilarity, we present several numerical experiments. In particular, we show that the underlying structure of the logistic map is picked out by the self‐dissimilarity signature of time series produced by that map. © 2007 Wiley Periodicals, Inc. Complexity 12: 77–85, 2007     

Global controllability between steady supercritical flows in channel networks

We consider a tree‐like network of open channels with outflow at the root. Controls are exerted at the boundary nodes of the network except for the root. In each channel, the flow is modelled by the de St. Venant equations. The node conditions require the conservation of mass and the conservation of energy. We show that the states of the system can be controlled within the entire network in finite time from a stationary supercritical initial state to a given supercritical terminal state with the same orientation. During this transition, the states stay in the class of C1‐functions, so no shocks occur. Copyright 2004 John Wiley & Sons, Ltd.     

Memory and a priori best strategy in complex adaptive systems

We employ an agent‐based model to show that memory and the absence of an a priori best strategy are sufficient for self‐segregation and clustering to emerge in a complex adaptive system with discrete agents that do not compete over a limited resource nor contend in a winner‐take‐all scenario. An agent starts from a corner of a two‐dimensional lattice and aims to reach a randomly selected site in the opposite side within the shortest possible time. The agent is isolated during the course of its journey and does not interact with other agents. Time‐bound obstacles appear at random lattice locations and the agent must decide whether to challenge or evade any obstacle blocking its path. The agent is capable of adapting a strategy in dealing with an obstacle. We analyze the dependence of strategy‐retention time with strategy for both memory‐based and memory‐less agents. We derive the equality spectrum to establish the environmental conditions that favor the existence of an a priori best strategy. We found that memory‐less agents do not polarize into two opposite strategy‐retention time distributions nor cluster toward a center distribution. © 2004 Wiley Periodicals, Inc. Complexity 9: 41–46, 2004     

BML revisited: Statistical physics,computer simulation,and probability

Statistical physics, computer simulation, and discrete mathematics are intimately related through the study of shared lattice models. These models lie at the foundation of all three fields, are studied extensively, and can be highly influential. Yet new computational and mathematical tools may challenge even well‐established beliefs. Consider the BML model, which is a paradigm for modeling self‐organized patterns of traffic flow and first‐order jamming transitions. Recent findings, on the existence of intermediate states, bring into question the standard understanding of the jamming transition. We review the results and show that the onset of full‐jamming can be considerably delayed based on the geometry of the system. We also introduce an asynchronous version of BML, which lacks the self‐organizing properties of BML, has none of the puzzling intermediate states, but has a sharp, discontinuous, transition to full jamming. We believe this asynchronous version will be more amenable to rigorous mathematical analysis than standard BML. We discuss additional models, such as bootstrap percolation, the honey‐comb dimer model and the rotor‐router, all of which exemplify the interplay between the three fields, while also providing cautionary tales. Finally, we synthesize implications for how results from one field may relate to the other, and also implications specific to computer implementations. © 2006 Wiley Periodicals, Inc. Complexity, 12, 30–39, 2006     

Well‐posedness of Compressible Euler Equations in a Physical Vacuum

An important problem in gas and fluid dynamics is to understand the behavior of vacuum states, namely the behavior of the system in the presence of a vacuum. In particular, physical vacuum, in which the boundary moves with a nontrivial finite normal acceleration, naturally arises in the study of the motion of gaseous stars or shallow water. Despite its importance, there are only a few mathematical results available near a vacuum. The main difficulty lies in the fact that the physical systems become degenerate along the vacuum boundary. In this paper, we establish the local‐in‐time well‐posedness of three‐dimensional compressible Euler equations for polytropic gases with a physical vacuum by considering the problem as a free boundary problem. © 2015 Wiley Periodicals, Inc.     

Unilateral Constrained Bending Vibrations on a Torsional String

Vibrations in long torsional strings result in spatio‐temporal dynamics. In order to actively damp these vibrations the system has to be analysed analytically, numerically and experimentally. Stick‐slip‐effects result in torsional selfexcited vibrations of the string. These vibrations are coupled with bending vibrations which are constrained by the borehole. The straight string was modelled in an experimental setup. The control of the straight string and the unilateral constrained bending vibrations were treated seperately. The dynamics of straight strings were controlled using three different approaches: firstly, a simple PD‐controller with the parameters calculated based on a one‐degree‐of‐freedom oscillator, secondly, the parameters were optimized using a simplex‐method, thirdly, the Karhunen‐Loeve‐transformation was used in order to reduce the dimension of the system. A controller based on the reduced system was implemented and the parameters were optimized with the same simplex algorithm. The unilateral constrained bending motion were examined at a cantilever beam which was assumed to be constrained in one direction in the middle of the beam. First, the beam was modelled analytically as a continuous system. The two states (contact and no contact) were described separately. The transition between these states were modelled with energy assumptions. Second, the beam was modelled as a Finite‐Element‐System. The numerical results of both methods were compared with experimental data.