Understanding Complexity in Biophysical Chemistry

Larter, Raima

doi:10.1021/jp020856l

Cited by 19 publications

(12 citation statements)

References 153 publications

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“…9 In their Fig. 6, Steinmetz et al 27 show a sequence of oscillations obtained while holding k 1 ¼ 0.35 fixed.…”

Section: Nested Arithmetic Progressionsmentioning

confidence: 94%

“…When plotting time evolutions, integrations were started from the arbitrary point (A, B, X, Y) ¼ (1, 1, 0.01, 0.01), maintaining all other conditions above. Following earlier works, 9,23,27 we select the following default values when parameters are not varying:…”

Section: Computational Detailsmentioning

confidence: 99%

“…For almost two centuries, chemical and biochemical reaction systems have been notorious sources of rich behaviors such as periodic, 1,2 self-pulsating, bursting, and chaotic oscillations. [3][4][5][6][7][8][9][10] A plethora of complex dynamical behaviors are typically present in enzymatic oscillators. 3 Among them, a prototypical system supporting intricate and exotic oscillatory modes is the PO reaction, namely, the aerobic oxidation of NADH catalyzed by the enzyme horseradish peroxidase.…”

Section: Introductionmentioning

confidence: 99%

“…The reaction mechanism of the PO system has been extensively investigated during the last decades. [6][7][8][9][10][11][12][13][14][15] The PO system has been also object of experimental investigations [16][17][18] and, for example, an experimentally determined stability diagram for the system is known in the control plane spanned by the NADH influx rate and the pH value of the medium. 18 Recently, the structural organization of this control plane was the object of a detailed numerical investigation, 19 based on a mechanism due to Bronnikova, Fedkina, Schaffer, and Olsen, 20 the so-called BFSO model.…”

Section: Introductionmentioning

confidence: 99%

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Nested arithmetic progressions of oscillatory phases in Olsen's enzyme reaction model

Gallas

2015

Chaos: An Interdisciplinary Journal of Nonlinear Science

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We report some regular organizations of stability phases discovered among self-sustained oscillations of a biochemical oscillator. The signature of such organizations is a nested arithmetic progression in the number of spikes of consecutive windows of periodic oscillations. In one of them, there is a main progression of windows whose consecutive number of spikes differs by one unit. Such windows are separated by a secondary progression of smaller windows whose number of spikes differs by two units. Another more complex progression involves a fan-like nested alternation of stability phases whose number of spikes seems to grow indefinitely and to accumulate methodically in cycles. Arithmetic progressions exist abundantly in several control parameter planes and can be observed by tuning just one among several possible rate constants governing the enzyme reaction.

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“…9 In their Fig. 6, Steinmetz et al 27 show a sequence of oscillations obtained while holding k 1 ¼ 0.35 fixed.…”

Section: Nested Arithmetic Progressionsmentioning

confidence: 94%

Section: Computational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Nested arithmetic progressions of oscillatory phases in Olsen's enzyme reaction model

Gallas

2015

Chaos: An Interdisciplinary Journal of Nonlinear Science

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“…Biochemical oscillations at the cellular level, also analyzed in terms of nonlinear dynamics, are described in the monograph by Goldbeter [54]. Furthermore, application of nonlinear dynamics in biophysical chemistry, including the effects of non-uniform fields on membrane transport, neuronal systems, calcium signaling, as well as the peroxidase-oxidase oscillator, was summarized by Larter in her later review [55]. Also, membrane oscillations and ion transport were reviewed by Kihara and Maeda [56] with the intention of extracting the fundamental information significant for understanding of oscillations at biomembranes in …”

Section: Biochemical Membrane Oscillatorsmentioning

confidence: 99%

Liquid Membrane and Other Membrane Oscillators

Orlik

2012

Self-Organization in Electrochemical Systems II

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In complement to the hydrodynamic instabilities driven by surface tension gradients, enclosed in Sects. 5.4-5.7, we describe here the dynamics of the liquid-liquid interface, formed by two fluids of very limited miscibility, e.g., by water and 2-nitropropane. First reports on this type of dynamical systems have been published by Dupeyrat and Nakache [1,2], and later analogous studies were continued also by .A representative example of that type of the systems is the water-2-nitropropane system [3]. The key point is that each phase should contain the dissolved species that is significantly better soluble in the other phase. In this way the initial state of such system is far from equilibrium and the natural trend to decrease the free Gibbs energy is the flow of each dissolved species to the other phase. In the example described here, the aqueous phase contains initially the hexadecyltrimethylammonium bromide (or cetyltrimethylammonium bromide, CTAB) the large organic CTA + cation of which exhibits, due to its hydrophobicity, higher affinity to the organic phase. In turn, the phase of 2-nitropropane contains initially dissolved picric acid (HA), better soluble and also partly dissociating in water (pK a % 0.2).When these two phases are brought into contact, with the organic layer placed over the aqueous layer, the oppositely directed flows of CTAB and HPi begin. This transport is associated with subtle oscillations of various characteristics: pH of aqueous solution, interfacial potential drop (Fig. 6.1), and interfacial tension. The latter phenomena are easily detectable as visible oscillations of the meniscus at the interface of both liquids. It is interesting that under such non-equilibrium conditions the presence of surfactant (CTAB) does not depress the surface tension gradients, but on the contrary, it is responsible for their periodic temporal variations.Yoshikawa and Matsubara [3] have proposed the mechanism of these oscillatory phenomena. First, one should note that CTA + cations in both phases form micelles above certain critical CTA + concentrations. Those micelles exhibit inverted M. Orlik, Self-Organization in Electrochemical Systems II, Monographs in Electrochemistry,

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Influence of Micellar Propinquity on Dynamics of Ce(IV)‐Catalyzed BZ Oscillatory Reaction under Stirred Conditions

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Najar

Ashraf

et al. 2014

Int J of Chemical Kinetics

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Oscillating reactions often employed to mimic and understand complex dynamics in biological systems are known to be affected in aggregated host environments. The dynamic evolution of the oscillatory Belousov–Zhabotinsky (BZ) reaction upon addition of increasing amounts of anionic (sodium dodecylbenzenesulfonate; SDBS), cationic (hexadecyltrimethylammonium bromide; CTAB), nonionic (polyoxyethylene(20) cetyl ether; Brij58), and binary mixtures (CTAB + Brij58 and SDBS + Brij58) of surfactants was monitored using potentiometry at 25 and 35°C under stirred batch conditions. The experimental results reveal that the oscillatory parameters of the Ce(IV)‐catalyzed BZ reaction are significantly altered depending on the concentration and nature of restricted micellar host environments. In the presence of ionic surfactants, it is proposed that the evolution of the oscillatory BZ system may be due to atypical proficiency (related to hydrophobic and electrostatic interactions) of such organized self‐assemblies to affect the reactivity by selectively confiscating some key reacting species. However, the response of the BZ system to nonionic Brij58 was attributed to the reaction among the alcoholic functional groups of the surfactant with some vital species of the BZ reaction. Moreover, the nonionic + ionic binary surfactant systems exhibited behaviors representative of both the constitutive single surfactant systems.

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Understanding Complexity in Biophysical Chemistry

Cited by 19 publications

References 153 publications

Nested arithmetic progressions of oscillatory phases in Olsen's enzyme reaction model

Nested arithmetic progressions of oscillatory phases in Olsen's enzyme reaction model

Liquid Membrane and Other Membrane Oscillators

Influence of Micellar Propinquity on Dynamics of Ce(IV)‐Catalyzed BZ Oscillatory Reaction under Stirred Conditions

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