scholarly journals Deep Reaction Network Exploration at a Heterogeneous Catalytic Interface

2021 ◽  
Author(s):  
Qiyuan Zhao ◽  
Yinan Xu ◽  
Jeffrey Greeley ◽  
Brett Savoie
Keyword(s):  
Ad Hoc ◽  
Heterogeneous Systems ◽  
Reaction Network ◽  
System Size ◽  
Product Formation ◽  
Major Product ◽  
Ethylene Oligomerization ◽  
Reaction Networks ◽  
Heterogeneous Catalytic ◽  
Reaction Barriers

Characterizing the reaction energies and reaction barriers of complex reaction networks is central to catalyst development and optimization. Nevertheless, heterogeneous catalytic surfaces pose several unique challenges to automatic reaction network characterization, including large system sizes and open-ended reactant lists, that make ad hoc network construction and characterization the current state-of-the-art. Here we show how automated algorithms for exploring and characterizing reaction networks can be adapted to the constraints of heterogeneous systems using ethylene oligomerization on silica-supported single site Ga3+ catalysts as a model system. Using only graph-based rules for exploring the network and elementary constraints based on activation energy and system size for identifying network terminations, a comprehensive reaction network was generated for this system and validated against standard methods. The automated algorithm (re)discovers the classic Cossee-Arlman mechanism for this system that is hypothesized to drive major product formation while remarkably also predicting several new pathways for producing alkanes and coke precursors. This demonstration represents the largest heterogeneous catalyst (more than 50 atoms, with an open-ended pool of reactants) to be characterized using a quantum chemistry-based automated reaction method.

scholarly journals Uncertainty quantification for quantum chemical models of complex reaction networks

2016 ◽  
Vol 195 ◽  
pp. 497-520 ◽  
Author(s):  
Jonny Proppe ◽  
Tamara Husch ◽  
Gregor N. Simm ◽  
Markus Reiher
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
State Space ◽  
Time Scales ◽  
Reaction Network ◽  
Reaction Networks ◽  
Multiple Time Scales ◽  
Complex Reaction ◽  
Discrete State ◽  
Continuous State

For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.

Feedback mechanisms in mineral replacement networks: an experimental investigation of the ultramafic model system

2021 ◽  
Author(s):  
Ingvild Aarrestad ◽  
Oliver Plümper ◽  
Desiree Roerdink ◽  
Andreas Beinlich
Keyword(s):  
Reaction Rate ◽  
Energy Transport ◽  
Kinetic Modelling ◽  
Indirect Evidence ◽  
Reaction Network ◽  
Reaction Networks ◽  
Silicate System ◽  
Rock Interaction ◽  
Feedback Mechanisms ◽  
Salinity Effect

<p>The overall rates of multi-component reaction networks are known to be controlled by feedback mechanisms. Feedback mechanisms represent loop systems where the output of the system is conveyed back as input and the system is either accelerated or regulated (positive and negative feedback respectively). In other words, feedback mechanisms control the rate of a reaction network without external influences. Feedback mechanisms are well-studied in a variety of reaction networks (e.g. bio-chemical, atmospheric); however, in fluid-rock interaction systems they are not researched as such. Still, indirect evidence, theoretical considerations and direct observations attest to their existence [e.g. 1, 2, 3]. It remains unknown how mass and energy transport between distinct reaction sites affect the overall reaction rate and outcome through feedback mechanisms. We propose that feedback mechanisms are a missing critical ingredient to understand reaction progress and timescales of fluid-rock interactions. We apply the serpentinization of ultramafic silicates as a relatively simple reaction network to investigate feedback mechanisms during fluid-rock interactions. Recent studies show that theoretical timescale-predictions appear inconsistent with natural observations [e.g. 4, 5]. The ultramafic silicate system is ideal for investigating feedback mechanisms as it is relevant to natural processes, is reactive on timescales that can be explored in the laboratory, and natural peridotite typically consists of less than four phases. Our preliminary observations indicate a feedback between pyroxene dissolution and olivine serpentinization. Olivine serpentinization appears to proceed faster in the presence of pyroxene. Furthermore, the bulk system reaction rate increases with increasing fluid salinity, which is opposite to the salinity effect on the monomineralic olivine system. Dunite (>90% olivine) is rare, which is why it is crucial to explore the more common pyroxene-bearing systems. The salinity effect is important to investigate due to the inevitable increase in fluid salinity from the boiling-induced phase separation and OH-uptake in the formation of serpentine. Here we present preliminary textural and chemical observations, which will subsequently be used for kinetic modelling of feedback.</p><p>[1] Ortoleva P., Merino, E., Moore, C. & Chadam, J. (1987). American Journal of Science <strong>287</strong>, 997-1007.</p><p>[2] Centrella, S., Austrheim, H., & Putnis, A. (2015). Lithos <strong>236–237</strong>, 245–255.</p><p>[3] Nakatani, T. & Nakamura, M. (2016). Geochemistry, Geophysics, Geosystems <strong>17</strong>, 3393-3419.</p><p>[4] Ingebritsen, S. E. & Manning, C. E. (2010). Geofluids <strong>10</strong>, 193-205.</p><p>[5] Beinlich, A., John, T., Vrijmoed, J.C., Tominaga, M., Magna, T. & Podladchikov, Y.Y. (2020). Nature Geoscience <strong>13</strong>, 307–311.</p>

scholarly journals Multiscale and Innovative Kinetic Approaches in Heterogeneous Catalysis

Catalysts ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 501
Author(s):  
Yves Schuurman ◽  
Pascal Granger
Keyword(s):  
Heterogeneous Catalysis ◽  
Catalytic Reactions ◽  
Reaction Networks ◽  
Complex Reaction ◽  
Reactor Modeling ◽  
Heterogeneous Catalytic

Kinetics and reactor modeling for heterogeneous catalytic reactions are prominent tools for investigating, and understanding, the catalyst functionalities at nanoscale, and related rates of complex reaction networks [...]

scholarly journals Oscillatory Adsorption as the Determinant of the Fluctuating Behaviour of Different Heterogeneous Systems

2000 ◽  
Vol 18 (1) ◽  
pp. 15-25 ◽  
Author(s):  
Kazymyr Patrylak ◽  
Lyubov Patrylak ◽  
Oleg Taranookha
Keyword(s):  
Phase Transitions ◽  
Chemical Interaction ◽  
Heterogeneous Systems ◽  
Oscillatory Process ◽  
Oscillatory Circuit ◽  
Electromagnetic System ◽  
Oscillatory Systems ◽  
Heterogeneous Catalytic ◽  
Oxidation Reduction ◽  
Oscillatory Reactions

Heterogeneous, catalytic oscillatory reactions as well as the oscillatory process of complex formation based on solid urea have been analysed in an attempt to ascertain the cause of such oscillatory mechanisms. In this context, oscillatory adsorption/desorption, phase transitions of the supported metal employed as the catalyst in the relevant oscillatory oxidation–reduction reactions as well as the reactions themselves have been considered. Based on an analysis of two oscillatory systems, of which one (i.e. the oscillatory alkylation of isobutane with butenes on a metal-free zeolite catalyst) is not complicated by any phase transitions, whilst the other (i.e. the oscillatory formation of an urea–octane complex via the interaction of urea with a binary vapour mixture of octane and non-complex-forming hydrocarbons) is not complicated by any chemical reactions, it is possible to infer that the source of the oscillatory properties of heterogeneous systems which involve the chemical interaction of their components is oscillatory adsorption which occurs as an uncomplicated self-supporting process which appears to proceed without any increase in the entropy of the system. The occurrence of oscillatory adsorption in a heterogeneous system leads to an oscillatory behaviour in the corresponding process, involving its simultaneous retardation in a similar manner as does the pendulum of a clock with respect to the untwisting of a spring or the oscillatory circuit of an electromagnetic system with respect to the discharge of a dry battery.

scholarly journals A compositional framework for reaction networks

2017 ◽  
Vol 29 (09) ◽  
pp. 1750028 ◽  
Author(s):  
John C. Baez ◽  
Blake S. Pollard
Keyword(s):  
Dynamical System ◽  
Steady State ◽  
General Framework ◽  
Nonlinear Dynamical System ◽  
Reaction Network ◽  
Reaction Networks ◽  
Nonlinear Dynamical ◽  
Input And Output ◽  
Open Dynamical System ◽  
Steady State Solutions

Reaction networks, or equivalently Petri nets, are a general framework for describing processes in which entities of various kinds interact and turn into other entities. In chemistry, where the reactions are assigned ‘rate constants’, any reaction network gives rise to a nonlinear dynamical system called its ‘rate equation’. Here we generalize these ideas to ‘open’ reaction networks, which allow entities to flow in and out at certain designated inputs and outputs. We treat open reaction networks as morphisms in a category. Composing two such morphisms connects the outputs of the first to the inputs of the second. We construct a functor sending any open reaction network to its corresponding ‘open dynamical system’. This provides a compositional framework for studying the dynamics of reaction networks. We then turn to statics: that is, steady state solutions of open dynamical systems. We construct a ‘black-boxing’ functor that sends any open dynamical system to the relation that it imposes between input and output variables in steady states. This extends our earlier work on black-boxing for Markov processes.

scholarly journals A Chemically Consistent Graph Architecture for Massive Reaction Networks Applied to Solid-Electrolyte Interphase Formation

2020 ◽  
Author(s):  
Samuel Blau ◽  
Hetal Patel ◽  
Evan Spotte-Smith ◽  
Xiaowei Xie ◽  
Shyam Dwaraknath ◽  
...  
Keyword(s):  
Solid Electrolyte ◽  
First Principles ◽  
Low Cost ◽  
Solid Electrolyte Interphase ◽  
Negative Electrode ◽  
Reaction Network ◽  
Reaction Networks ◽  
Graph Representations ◽  
Li Ion ◽  
Shortest Path Algorithms

Modeling reactivity with chemical reaction networks could yield fundamental mechanistic understanding that would expedite the development of processes and technologies for energy storage, medicine, catalysis, and more. Thus far, reaction networks have been limited in size by chemically inconsistent graph representations of multi-reactant reactions (e.g. A + B reacts to C) that cannot enforce stoichiometric constraints, precluding the use of optimized shortest-path algorithms. Here, we report a chemically consistent graph architecture that overcomes these limitations using a novel multi-reactant representation and iterative cost-solving procedure. Our approach enables the identification of all low-cost pathways to desired products in massive reaction networks containing reactions of any stoichiometry, allowing for the investigation of vastly more complex systems than previously possible. Leveraging our architecture, we construct the first ever electrochemical reaction network from first-principles thermodynamic calculations to describe the formation of the Li-ion solid electrolyte interphase (SEI), which is critical for passivation of the negative electrode. Using this network comprised of nearly 6,000 species and 4.5 million reactions, we interrogate the formation of a key SEI component, lithium ethylene dicarbonate. We automatically identify previously proposed mechanisms as well as multiple novel pathways containing counter-intuitive reactions that have not, to our knowledge, been reported in the literature. We envision that our framework and data-driven methodology will facilitate efforts to engineer the composition-related properties of the SEI - or of any complex chemical process - through selective control of reactivity.

scholarly journals A general technique for the detection of switch-like bistability in chemical reaction networks governed by mass action kinetics with conservation laws

2020 ◽  
Author(s):  
Brandon C Reyes ◽  
Irene Otero-Muras ◽  
Vladislav A Petyuk
Keyword(s):  
Conservation Laws ◽  
Signaling Pathways ◽  
Chemical Reaction ◽  
Reaction Network ◽  
Mass Action ◽  
Numerical Continuation ◽  
Reaction Networks ◽  
General Technique ◽  
Bistable Switch ◽  
Mass Action Kinetics

AbstractBackgroundTheoretical analysis of signaling pathways can provide a substantial amount of insight into their function. One particular area of research considers signaling pathways capable of assuming two or more stable states given the same amount of signaling ligand. This phenomenon of bistability can give rise to switch-like behavior, a mechanism that governs cellular decision making. Investigation of whether or not a signaling pathway can confer bistability and switch-like behavior, without knowledge of specific kinetic rate constant values, is a mathematically challenging problem. Recently a technique based on optimization has been introduced, which is capable of finding example parameter values that confer switch-like behavior for a given pathway. Although this approach has made it possible to analyze moderately sized pathways, it is limited to reaction networks that presume a uniterminal structure. It is this limited structure we address by developing a general technique that applies to any mass action reaction network with conservation laws.ResultsIn this paper we developed a generalized method for detecting switch-like bistable behavior in any mass action reaction network with conservation laws. The method involves 1) construction of a constrained optimization problem using the determinant of the Jacobian of the underlying rate equations, 2) minimization of the objective function to search for conditions resulting in a zero eigenvalue 3) computation of a confidence level that describes if the global minimum has been found and 4) evaluation of optimization values, using either numerical continuation or directly simulating the ODE system, to verify that a bistability region exists. The generalized method has been tested on three motifs known to be capable of bistability.ConclusionsWe have developed a variation of an optimization-based method for discovery of bistability, which is not limited to the structure of the chemical reaction network. Successful completion of the method provides an S-shaped bifurcation diagram, which indicates that the network acts as a bistable switch for the given optimization parameters.

scholarly journals On reaction network implementations of neural networks

2021 ◽  
Vol 18 (177) ◽  
Author(s):  
David F. Anderson ◽  
Badal Joshi ◽  
Abhishek Deshpande
Keyword(s):  
Neural Networks ◽  
Fixed Points ◽  
Reaction Network ◽  
Activation Function ◽  
Reaction Networks ◽  
Mathematical Framework ◽  
Feed Forward Neural Networks ◽  
Systems Of Odes ◽  
Do So

This paper is concerned with the utilization of deterministically modelled chemical reaction networks for the implementation of (feed-forward) neural networks. We develop a general mathematical framework and prove that the ordinary differential equations (ODEs) associated with certain reaction network implementations of neural networks have desirable properties including (i) existence of unique positive fixed points that are smooth in the parameters of the model (necessary for gradient descent) and (ii) fast convergence to the fixed point regardless of initial condition (necessary for efficient implementation). We do so by first making a connection between neural networks and fixed points for systems of ODEs, and then by constructing reaction networks with the correct associated set of ODEs. We demonstrate the theory by constructing a reaction network that implements a neural network with a smoothed ReLU activation function, though we also demonstrate how to generalize the construction to allow for other activation functions (each with the desirable properties listed previously). As there are multiple types of ‘networks’ used in this paper, we also give a careful introduction to both reaction networks and neural networks, in order to disambiguate the overlapping vocabulary in the two settings and to clearly highlight the role of each network’s properties.

scholarly journals Influence of Structure Sensitivity on Apparent Activation Energy of Parallel Heterogeneous Catalytic Reactions

2019 ◽  
Vol 150 (6) ◽  
pp. 1561-1570
Author(s):  
Dmitry Yu. Murzin
Keyword(s):  
Activation Energy ◽  
Theoretical Analysis ◽  
Apparent Activation Energy ◽  
Continuous Distribution ◽  
Reaction Network ◽  
Catalytic Reactions ◽  
Irreversible Adsorption ◽  
Active Centers ◽  
Heterogeneous Catalytic ◽  
Parallel Reactions

Abstract Analysis of apparent activation energy is presented for different heterogeneous catalytic reactions with parallel reaction routes. In the case of kinetic coupling between catalytic cycles the activation energy in a particular route depends not only on the activation energies of the elementary steps comprising this route, but also on the frequency of the steps in a parallel route. Expressions were derived for coupling between routes through irreversible adsorption of the substrate, quasi-equilibrated binding as well as different substrate adsorption modes. Theoretical analysis of the apparent activation energy was extended for the reaction network with two routes possessing mechanistically different rate determining steps (i.e. monomolecular vs bimolecular). For structure sensitive reactions an expression for the apparent activation energy for parallel reactions was developed for cases with a continuous distribution of active centers and a cubo-octahedral representation of the metal clusters. A comparison between the theoretical analysis and experimental data on transformations of furfural to furfuryl alcohol and furan on ruthenium clusters shows applicability of the developed theoretical framework. Graphic Abstract

scholarly journals Early warning signals in chemical reaction networks

2020 ◽  
Vol 56 (26) ◽  
pp. 3725-3728
Author(s):  
Oliver R. Maguire ◽  
Albert S. Y. Wong ◽  
Jan Harm Westerdiep ◽  
Wilhelm T. S. Huck
Keyword(s):  
Complex Systems ◽  
Chemical Reaction ◽  
Early Warning ◽  
Reaction Network ◽  
Chemical Reaction Networks ◽  
Chemical Reaction Network ◽  
Reaction Networks ◽  
Warning Signals ◽  
Early Warning Signals ◽  
Complex Chemical

Many natural and man-made complex systems display early warning signals when close to an abrupt shift in behaviour. Here we show that such early warning signals appear in a complex chemical reaction network.

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