Fast reactions with non-interacting species in stochastic reaction networks

<abstract><p>We consider stochastic reaction networks modeled by continuous-time Markov chains. Such reaction networks often contain many reactions, potentially occurring at different time scales, and have unknown parameters (kinetic rates, total amounts). This makes their analysis complex. We examine stochastic reaction networks with non-interacting species that often appear in examples of interest (e.g. in the two-substrate Michaelis Menten mechanism). Non-interacting species typically appear as intermediate (or transient) chemical complexes that are depleted at a fast rate. We embed the Markov process of the reaction network into a one-parameter family under a two time-scale approach, such that molecules of non-interacting species are degraded fast. We derive simplified reaction networks where the non-interacting species are eliminated and that approximate the scaled Markov process in the limit as the parameter becomes small. Then, we derive sufficient conditions for such reductions based on the reaction network structure for both homogeneous and time-varying stochastic settings, and study examples and properties of the reduction.</p></abstract>

Higher Dependency on Visual Inputs During Posture Control: Another Long-Term Effect of mTBIs

This study investigated the hypothesis that individuals living with long-term effects of mild traumatic brain injury (mTBI) develop increased dependency on their visual inputs to control their vertical posture. To test this hypothesis we quantified visuo-postural dependency indices (VPDIs) calculated independently for multiple postural behavioral markers extracted from the body’s center of pressure coordinates signals recorded during the execution of a quiet bipedal stance. One hundred and twenty-nine volunteers participated in this study. An mTBI (n = 50) and a neurotypical Control group were formed (n = 79). VPDIs were calculated as the normalized pair-wise subtraction of recordings obtained under Vision and No-Vision experimental conditions. Consistent with our hypothesis the results of this study show that balance behavior of mTBI participants deteriorate more abruptly in the absence of visual inputs when compared to neurotypical controls. These impairments may increase the likelihood of recurrent traumas when fast reactions are needed in daily activities, sports practice, or military operations. Additionally, the methodology used in this study showed to be potentially useful to aid future investigations of neural circuitry impaired by mTBI and provide indices of recovery in future clinical trials testing mTBI-related clinical interventions.

Numerical studies of higher order tau-leaping methods

Gillespie's algorithm, also known as the Stochastic Simulation Algorithm (SSA), is an exact simulation method for the Chemical Master Equation model of well-stirred biochemical systems. However, this method is computationally intensive when some fast reactions are present in the system. The tau-leap scheme developed by Gillespie can speed up the stochastic simulation of these biochemically reacting systems with negligible loss in accuracy. A number of tau-leaping methods were proposed, including the explicit tau-leaping and the implicit tau-leaping strategies. Nonetheless, these schemes have low order of accuracy. In this thesis, we investigate tau-leap strategies which achieve high accuracy at reduced computational cost. These strategies are tested on several biochemical systems of practical interest.

Numerical studies of higher order tau-leaping methods

Gillespie's algorithm, also known as the Stochastic Simulation Algorithm (SSA), is an exact simulation method for the Chemical Master Equation model of well-stirred biochemical systems. However, this method is computationally intensive when some fast reactions are present in the system. The tau-leap scheme developed by Gillespie can speed up the stochastic simulation of these biochemically reacting systems with negligible loss in accuracy. A number of tau-leaping methods were proposed, including the explicit tau-leaping and the implicit tau-leaping strategies. Nonetheless, these schemes have low order of accuracy. In this thesis, we investigate tau-leap strategies which achieve high accuracy at reduced computational cost. These strategies are tested on several biochemical systems of practical interest.

Mechanism of the oxidation of nitric oxide with oxygen

Very fast reactions of forming higher nitrogen oxides set out an equilibrium framework for the course of the reaction of nitrogen monoxide oxidation. The slow course of reaction of nitrogen monoxide with oxygen permanently violates the created equilibria. In particular, the equilibrium of the oxidation reaction of nitrogen monoxide with nitrogen dioxide. The contribution of this reaction to the transformation of nitrogen monoxide in the conditions of nitrogen trioxide removal from the gas phase was estimated.

Age Effects on Distraction in a Visual Task Requiring Fast Reactions: An Event-Related Potential Study

We investigated the effects of distractors in older and younger participants in choice and simple reaction time tasks with concurrent registration of event-related potentials. In the task the participants had to prevent a disk from falling into a bin after a color or luminosity change (target stimuli). Infrequently, task-irrelevant stimuli (schematic faces or threatening objects) were superimposed on the target stimuli (distractors), or the bin disappeared which required no response (Nogo trials). Reaction time was delayed to the distractors, but this effect was similar in the two age groups. As a robust age-related difference, in the older group a large anterior positivity and posterior negativity emerged to the distractors within the 100–200 ms post-stimulus range, and these components were larger for schematic faces than for threatening objects. sLORETA localized the age-specific effect to the ventral stream of the visual system and to anterior structures considered as parts of the executive system. The Nogo stimuli elicited a late positivity (Nogo P3) with longer latency in the older group. We interpreted the age-related differences as decreased but compensated resistance to task-irrelevant change of the target stimuli.

Fast moving horizon estimation using multi-level iterations for microgrid control

Accurate state-estimation is a vital prerequisite for fast feedback control methods such as Nonlinear Model Predictive Control (NMPC). For efficient process control, it is of great importance that the estimation process is carried out as fast as possible to provide the feedback mechanism with fresh information and enable fast reactions in case of any disturbances. We discuss how Multi-Level Iterations (MLI), known from NMPC, can be applied to the Moving Horizon Estimation (MHE) method for estimating the states and parameters of a system described by a Differential Algebraic Equation model. A challenging field of application for the proposed MLI-MHE method are electric microgrids. These push current control approaches to their limits due to the rising penetration of volatile renewable energy sources and the fast electrical system dynamics. We investigate the closed-loop control performance of the proposed MLI-MHE algorithm in combination with an NMPC controller for a realistic sized microgrid as a numerical example.

Chemical Reactivities of ortho-Quinones Produced in Living Organisms: Fate of Quinonoid Products Formed by Tyrosinase and Phenoloxidase Action on Phenols and Catechols

Tyrosinase catalyzes the oxidation of phenols and catechols (o-diphenols) to o-quinones. The reactivities of o-quinones thus generated are responsible for oxidative browning of plant products, sclerotization of insect cuticle, defense reaction in arthropods, tunichrome biochemistry in tunicates, production of mussel glue, and most importantly melanin biosynthesis in all organisms. These reactions also form a set of major reactions that are of nonenzymatic origin in nature. In this review, we summarized the chemical fates of o-quinones. Many of the reactions of o-quinones proceed extremely fast with a half-life of less than a second. As a result, the corresponding quinone production can only be detected through rapid scanning spectrophotometry. Michael-1,6-addition with thiols, intramolecular cyclization reaction with side chain amino groups, and the redox regeneration to original catechol represent some of the fast reactions exhibited by o-quinones, while, nucleophilic addition of carboxyl group, alcoholic group, and water are mostly slow reactions. A variety of catecholamines also exhibit side chain desaturation through tautomeric quinone methide formation. Therefore, quinone methide tautomers also play a pivotal role in the fate of numerous o-quinones. Armed with such wide and dangerous reactivity, o-quinones are capable of modifying the structure of important cellular components especially proteins and DNA and causing severe cytotoxicity and carcinogenic effects. The reactivities of different o-quinones involved in these processes along with special emphasis on mechanism of melanogenesis are discussed.