Diffusion Controlled Reactions, Fluctuation Dominated Kinetics, and Living Cell Biochemistry

Konkoli, Zoran

doi:10.4204/eptcs.9.11

Cited by 7 publications

(7 citation statements)

References 21 publications

(49 reference statements)

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“…The lattice model with local coupling used in this study has been used to simulate the diffusion of biological active substances (Konkoli, ; Schmit et al ., ). Our numerical simulation with phase‐shifting interactions between neighboring oscillators where SPOs were confined to a small region reproduced a phase wave in the SCN, which started from the SPR and spread to other SCN regions.…”

Section: Discussionmentioning

confidence: 99%

Regional circadian period difference in the suprachiasmatic nucleus of the mammalian circadian center

Koinuma

Asakawa

Nagano

et al. 2013

Eur J of Neuroscience

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The suprachiasmatic nucleus (SCN) is the mammalian circadian rhythm center. Individual oscillating neurons have different endogenous circadian periods, but they are usually synchronized by an intercellular coupling mechanism. The differences in the period of each oscillating neuron have been extensively studied; however, the clustering of oscillators with similar periods has not been reported. In the present study, we artificially disrupted the intercellular coupling among oscillating neurons in the SCN and observed regional differences in the periods of the oscillating small-latticed regions of the SCN using a transgenic rat carrying a luciferase reporter gene driven by regulatory elements from a per2 clock gene (Per2::dluc rat). The analysis divided the SCN into two regions--aregion with periods shorter than 24 h (short-period region, SPR) and another with periods longer than 24 h (long-period region, LPR). The SPR was located in the smaller medial region of the dorsal SCN, whereas the LPR occupied the remaining larger region. We also found that slices containing the medial region of the SCN generated shorter circadian periods than slices that contained the lateral region of the SCN. Interestingly, the SPR corresponded well with the region where the SCN phase wave is generated. We numerically simulated the relationship between the SPR and a large LPR. A mathematical model of the SCN based on our findings faithfully reproduced the kinetics of the oscillators in the SCN in synchronized conditions, assuming the existence of clustered short-period oscillators.

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Section: Discussionmentioning

confidence: 99%

Regional circadian period difference in the suprachiasmatic nucleus of the mammalian circadian center

Koinuma

Asakawa

Nagano

et al. 2013

Eur J of Neuroscience

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“…The reactions outlined in Table 2 describe direct dissociation radiation-induced reactions, bimolecular reactions within the ice, and some desorption reactions driven by incoming radiation. An interesting point to consider is that these bimolecular reactions induced by incoming radiation could be related to diffusion-controlled bimolecular reactions (e.g., Shoup et al 1981;Rice 1985;Burschka 1997;Atkins 1998;Konkoli 2009) because the incoming radiation supplies energy to the embedded species and makes them able to diffuse through the ice. Further research can explore the relationship between these two parameters, as well as the association between ERCs of the bimolecular reactions and other properties such as reaction binding energies, molecular diffusion, and viscosity.…”

Section: Evolution Of Molecular Abundances and Calculation Of Ercsmentioning

confidence: 99%

Understanding the Molecular Kinetics and Chemical Equilibrium Phase of Frozen CO during Bombardment by Cosmic Rays by Employing the PROCODA Code

Pilling

Carvalho

Abreu

et al. 2023

ApJ

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Within the cold regions of space, ices that are enriched with carbon monoxide (CO) molecules are exposed to ionizing radiation, which triggers new reactions and desorption processes. Laboratory studies on astrochemical ices employing different projectiles have revealed the appearance of several new species. In this study, we employed the upgraded PROCODA code, which involves a calculation phase utilizing thermochemistry data, to map the chemical evolution of pure CO ice irradiated by cosmic-ray analogs. In the model, we have considered 18 different chemical species (six observed: CO, CO2, C3, O3, C2O, and C5O3; 12 unobserved: C, O, C2, O2, CO3, C3O, C4O, C5O, C2O2, C2O3, C3O2, and C4O2) coupled at 156 reaction routes. Our best-fit model provides effective reaction rates (effective rate constants, (ERCs)), branching ratios for reactions within reaction groups, several desorption parameters, and the characterization of molecular abundances at the chemical equilibrium (CE) phase. The most abundant species within the ice at the CE phase were atomic oxygen (68.2%) and atomic carbon (18.2%), followed by CO (11.8%) and CO2 (1.6%). The averaged modeled desorption yield and rate were 1.3e5 molecules ion−1 and 7.4e13 molecules s−1, respectively, while the average value of ERCs in the radiation-induced dissociation reactions was 2.4e-1 s−1 and for the bimolecular reactions it was 4.4e-24 cm3 molecule−1 s−1. We believe that the current kinetics study can be used in future astrochemical models to better understand the chemical evolution of embedded species within astrophysical ices under the presence of an ionizing radiation field.

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“…The existence of this phenomenon has been known for more than three decades [24,29]. The effect of domain formation on reaction kinetics is weaker when the reaction system is represented in a three-dimensional space because of the increased degrees of freedom of movement for the particles, but it is still present [18,21,19]. In living cells, many reactions occur on two-dimensional surfaces, and, because of significant crowding in the cell, classical ODE rate laws may not be good models for many phenomena seen in vivo [26].…”

Section: Diffusion-limited Reactionsmentioning

confidence: 99%

Simulating Kinetic Processes in Time and Space on a Lattice

Gill¹,

Shaw²,

Rountree

et al. 2011

Math. Model. Nat. Phenom.

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Abstract. We have developed a chemical kinetics simulation that can be used as both an educational and research tool. The simulator is designed as an accessible, open-source project that can be run on a laptop with a student-friendly interface. The application can potentially be scaled to run in parallel for large simulations. The simulation has been successfully used in a classroom setting for teaching basic electrochemical properties. We have shown that this can be used for simulating fundamental molecular and chemical processes and even simplified models of predator-prey interactions. By giving the simulated entities spatial extent in the lattice, the particles do not interpenetrate, and clusters of particles can spatially exclude one another. Our simulation demonstrates that spatial inhomogeneity leads to different results than those that are obtained by using standard ordinary differential equation models, as previously reported.

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Diffusion Controlled Reactions, Fluctuation Dominated Kinetics, and Living Cell Biochemistry

Cited by 7 publications

References 21 publications

Regional circadian period difference in the suprachiasmatic nucleus of the mammalian circadian center

Regional circadian period difference in the suprachiasmatic nucleus of the mammalian circadian center

Understanding the Molecular Kinetics and Chemical Equilibrium Phase of Frozen CO during Bombardment by Cosmic Rays by Employing the PROCODA Code

Simulating Kinetic Processes in Time and Space on a Lattice

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