scholarly journals Searching for the origin of life using a computational search engine

2018 ◽  
Author(s):  
Jan H. Jensen
Keyword(s):  
Metabolic Pathways ◽  
Reaction Network ◽  
Building Blocks ◽  
Reaction Networks ◽  
Early Earth ◽  
Complex Reaction ◽  
Reaction Conditions ◽  
Computational Search ◽  
The Origin Of Life ◽  
Simple Molecules

Life is essentially an organised network of chemical reactions (metabolic pathways) that can create copies of itself given a source of energy. How was this complex reaction network formed from the simple molecules that were present on the early Earth? I will answer this question by simulating how simple reaction networks evolve starting from different combinations of building blocks and reaction conditions. Computer simulations will allow me to search many more combinations than is possible experimentally, thereby increasing the chances of finding reaction networks that resemble those found in modern cells. Finding a plausible explanation for how life originated on Earth will not only have profound implications for how we view ourselves and other species, but also give us a much better idea of how likely life is to have evolved on other planets.

scholarly journals Searching for the origin of life using a computational search engine

2018 ◽  
Author(s):  
Jan H. Jensen
Keyword(s):  
Metabolic Pathways ◽  
Reaction Network ◽  
Building Blocks ◽  
Reaction Networks ◽  
Early Earth ◽  
Complex Reaction ◽  
Reaction Conditions ◽  
Computational Search ◽  
The Origin Of Life ◽  
Simple Molecules

Life is essentially an organised network of chemical reactions (metabolic pathways) that can create copies of itself given a source of energy. How was this complex reaction network formed from the simple molecules that were present on the early Earth? I will answer this question by simulating how simple reaction networks evolve starting from different combinations of building blocks and reaction conditions. Computer simulations will allow me to search many more combinations than is possible experimentally, thereby increasing the chances of finding reaction networks that resemble those found in modern cells. Finding a plausible explanation for how life originated on Earth will not only have profound implications for how we view ourselves and other species, but also give us a much better idea of how likely life is to have evolved on other planets.

Photochemical Evolution of Interstellar/Precometary Organic Material

1997 ◽  
Vol 161 ◽  
pp. 23-47 ◽  
Author(s):  
Louis J. Allamandola ◽  
Max P. Bernstein ◽  
Scott A. Sandford
Keyword(s):  
Origin Of Life ◽  
Building Blocks ◽  
Complex Species ◽  
Infrared Observations ◽  
Interstellar Ice ◽  
Polycyclic Aromatic ◽  
Ultraviolet Photolysis ◽  
The Origin Of Life ◽  
Simple Molecules ◽  
Complex Organic

AbstractInfrared observations, combined with realistic laboratory simulations, have revolutionized our understanding of interstellar ice and dust, the building blocks of comets. Since comets are thought to be a major source of the volatiles on the primative earth, their organic inventory is of central importance to questions concerning the origin of life. Ices in molecular clouds contain the very simple molecules H2O, CH3OH, CO, CO2, CH4, H2, and probably some NH3and H2CO, as well as more complex species including nitriles, ketones, and esters. The evidence for these, as well as carbonrich materials such as polycyclic aromatic hydrocarbons (PAHs), microdiamonds, and amorphous carbon is briefly reviewed. This is followed by a detailed summary of interstellar/precometary ice photochemical evolution based on laboratory studies of realistic polar ice analogs. Ultraviolet photolysis of these ices produces H2, H2CO, CO2, CO, CH4, HCO, and the moderately complex organic molecules: CH3CH2OH (ethanol), HC(= O)NH2(formamide), CH3C(= O)NH2(acetamide), R-CN (nitriles), and hexamethylenetetramine (HMT, C6H12N4), as well as more complex species including polyoxymethylene and related species (POMs), amides, and ketones. The ready formation of these organic species from simple starting mixtures, the ice chemistry that ensues when these ices are mildly warmed, plus the observation that the more complex refractory photoproducts show lipid-like behavior and readily self organize into droplets upon exposure to liquid water suggest that comets may have played an important role in the origin of life.

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.

scholarly journals First Principles Micro-kinetic Model of Catalytic Non-oxidative Dehydrogenation of Ethane over Close-packed Metallic Facets

2019 ◽  
Author(s):  
Martin Hangaard Hansen ◽  
Jens K. Nørskov ◽  
Thomas Bligaard
Keyword(s):  
Kinetic Model ◽  
Oxidative Dehydrogenation ◽  
Reaction Network ◽  
Building Blocks ◽  
Light Olefins ◽  
Catalytic Dehydrogenation ◽  
Reaction Conditions ◽  
Model Code ◽  
Ethane Dehydrogenation ◽  
Oxidative Dehydrogenation Of Ethane

<div> <div> <p>Catalytic dehydrogenation of light alkanes may other more efficient routes to selectively producing light olefins, which are some of the most important chemical building blocks in the industry, in terms of scale. We present a descriptor based micro-kinetic model of the trends in selectivity and activity of non-oxidative dehydrogenation of ethane over close-packed metal facets and through varied reaction conditions. Our model predicts and explains the experimentally observed promotion effect on turnover rate from co-feeding hydrogen as an effect of the shifting equilibria in steady state. At low conversion reaction conditions over Pt, the path to ethene goes through ethane dehydrogenation to ethyl, CH 3 CH 2 *, then to ethene while the non-selective pathway to methane and deeply dehydrogenated species is predicted to go through dehydrogenation via CH 3 CH*. This implies that the desorption step of ethene is not the limiting step for selectivity and that geometric effects that stabilize CH 2 CH 2 * compared to CH 3 CH* are desirable properties of a better catalyst. Removing reactive bridge and 3-fold sites facilitates this, which may be achievable by sufficient concentrations of tin in platinum. The included model code furthermore provides a base for easy tuning and for expanding the study to other thermodynamic conditions, other facets, alloys or the reaction network to longer hydrocarbons or to oxidative pathways.</p> </div> </div>

scholarly journals Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research

2017 ◽  
Vol 13 ◽  
pp. 1388-1395 ◽  
Author(s):  
Ben Shirt-Ediss ◽  
Sara Murillo-Sánchez ◽  
Kepa Ruiz-Mirazo
Keyword(s):  
Evolutionary Dynamics ◽  
Prebiotic Chemistry ◽  
Difficult Problem ◽  
Evolutionary Development ◽  
Bulk Solution ◽  
Reaction Networks ◽  
Early Earth ◽  
Complex Reaction ◽  
Solution Sets ◽  
Living Organisms

Conceiving the process of biogenesis as the evolutionary development of highly dynamic and integrated protocell populations provides the most appropriate framework to address the difficult problem of how prebiotic chemistry bridged the gap to full-fledged living organisms on the early Earth. In this contribution we briefly discuss the implications of taking dynamic, functionally integrated protocell systems (rather than complex reaction networks in bulk solution, sets of artificially evolvable replicating molecules, or even these same replicating molecules encapsulated in passive compartments) as the proper units of prebiotic evolution. We highlight, in particular, how the organisational features of those chemically active and reactive protocells, at different stages of the process, would strongly influence their corresponding evolutionary capacities. As a result of our analysis, we suggest three experimental challenges aimed at constructing protocell systems made of a diversity of functionally coupled components and, thereby, at characterizing more precisely the type of prebiotic evolutionary dynamics that such protocells could engage in.

scholarly journals Activated Self-Resolution and Error-Correction in Catalytic Reaction Networks

2021 ◽  
Author(s):  
Fredrik Schaufelberger ◽  
Olof Ramstrom
Keyword(s):  
Dynamic System ◽  
Error Correction ◽  
Small Molecule ◽  
Catalytic Reaction ◽  
Reaction Network ◽  
Reaction Networks ◽  
Complex Reaction ◽  
Catalytic Systems ◽  
Systems Chemistry ◽  
Mbh Reaction

<p>To understand the emergence of function in complex reaction networks is a primary goal of systems chemistry and origin-of-life studies. Especially challenging is the establishment of systems that simultaneously exhibit several functionality parameters that can be independently tuned. In this work, a multifunctional complex reaction network of nucleophilic small molecule catalysts for the Morita-Baylis-Hillman (MBH) reaction is demonstrated. The dynamic system exhibited triggered self-resolution, preferentially amplifying a specific catalyst/product set out of a many potential alternatives. By utilizing selective reversibility of the products of the reaction set, systemic thermodynamically driven error-correction could also be introduced. To achieve this, a dynamic covalent MBH reaction based on adducts with internal H-transfer capabilities was developed, displaying rate accelerations of retro-MBH reactions up to 104 times. This study demonstrates how efficient self-sorting of catalytic systems can be achieved through an interplay of several complex emergent functionalities.</p>

scholarly journals Shock Processing of Amino Acids Leading to Complex Structures—Implications to the Origin of Life

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5634 ◽  
Author(s):  
Surendra V. Singh ◽  
Jayaram Vishakantaiah ◽  
Jaya K. Meka ◽  
Vijayan Sivaprahasam ◽  
Vijayanand Chandrasekaran ◽  
...  
Keyword(s):  
Amino Acids ◽  
Building Blocks ◽  
Form Complex ◽  
Shock Heating ◽  
The Origin Of Life ◽  
Simple Molecules ◽  
First Time ◽  
Shock Processing ◽  
Impact Events

The building blocks of life, amino acids, are believed to have been synthesized in the extreme conditions that prevail in space, starting from simple molecules containing hydrogen, carbon, oxygen and nitrogen. However, the fate and role of amino acids when they are subjected to similar processes largely remain unexplored. Here we report, for the first time, that shock processed amino acids tend to form complex agglomerate structures. Such structures are formed on timescales of about 2 ms due to impact induced shock heating and subsequent cooling. This discovery suggests that the building blocks of life could have self-assembled not just on Earth but on other planetary bodies as a result of impact events. Our study also provides further experimental evidence for the ‘threads’ observed in meteorites being due to assemblages of (bio)molecules arising from impact-induced shocks.

scholarly journals Activated Self-Resolution and Error-Correction in Catalytic Reaction Networks

2021 ◽  
Author(s):  
Fredrik Schaufelberger ◽  
Olof Ramstrom
Keyword(s):  
Dynamic System ◽  
Error Correction ◽  
Small Molecule ◽  
Catalytic Reaction ◽  
Reaction Network ◽  
Reaction Networks ◽  
Complex Reaction ◽  
Catalytic Systems ◽  
Systems Chemistry ◽  
Mbh Reaction

<p>To understand the emergence of function in complex reaction networks is a primary goal of systems chemistry and origin-of-life studies. Especially challenging is the establishment of systems that simultaneously exhibit several functionality parameters that can be independently tuned. In this work, a multifunctional complex reaction network of nucleophilic small molecule catalysts for the Morita-Baylis-Hillman (MBH) reaction is demonstrated. The dynamic system exhibited triggered self-resolution, preferentially amplifying a specific catalyst/product set out of a many potential alternatives. By utilizing selective reversibility of the products of the reaction set, systemic thermodynamically driven error-correction could also be introduced. To achieve this, a dynamic covalent MBH reaction based on adducts with internal H-transfer capabilities was developed, displaying rate accelerations of retro-MBH reactions up to 104 times. This study demonstrates how efficient self-sorting of catalytic systems can be achieved through an interplay of several complex emergent functionalities.</p>

A Derived Markov Process for Modeling Reaction Networks

2003 ◽  
Vol 11 (4) ◽  
pp. 339-362 ◽  
Author(s):  
John H. Holland
Keyword(s):  
Monte Carlo ◽  
Markov Process ◽  
Active Sites ◽  
Reaction Network ◽  
Building Blocks ◽  
Reaction Networks ◽  
Expected Time ◽  
Matrix Operations ◽  
First Occurrence ◽  
Economic Goods

A reaction network arises when a set of reactants (chromosomes, chemicals, economic goods, or the like) recombine at specified rates to produce other reactants in the set. When the reactants are characterized in terms of “reactive regions” (schemata, active sites, building blocks), reaction networks can be modeled by classic stochastic urn models. The corresponding Markov processes are specified by matrices that, for realistic problems, are small enough to allow standard matrix operations and Monte Carlo estimates of important properties of the trajectory of the process, such as the expected time to first occurrence of some designated reactant.

scholarly journals First Principles Micro-kinetic Model of Catalytic Non-oxidative Dehydrogenation of Ethane over Close-packed Metallic Facets

2019 ◽  
Author(s):  
Martin Hangaard Hansen ◽  
Jens K. Nørskov ◽  
Thomas Bligaard
Keyword(s):  
Kinetic Model ◽  
Oxidative Dehydrogenation ◽  
Reaction Network ◽  
Building Blocks ◽  
Light Olefins ◽  
Catalytic Dehydrogenation ◽  
Reaction Conditions ◽  
Model Code ◽  
Ethane Dehydrogenation ◽  
Oxidative Dehydrogenation Of Ethane

<div> <div> <p>Catalytic dehydrogenation of light alkanes may other more efficient routes to selectively producing light olefins, which are some of the most important chemical building blocks in the industry, in terms of scale. We present a descriptor based micro-kinetic model of the trends in selectivity and activity of non-oxidative dehydrogenation of ethane over close-packed metal facets and through varied reaction conditions. Our model predicts and explains the experimentally observed promotion effect on turnover rate from co-feeding hydrogen as an effect of the shifting equilibria in steady state. At low conversion reaction conditions over Pt, the path to ethene goes through ethane dehydrogenation to ethyl, CH 3 CH 2 *, then to ethene while the non-selective pathway to methane and deeply dehydrogenated species is predicted to go through dehydrogenation via CH 3 CH*. This implies that the desorption step of ethene is not the limiting step for selectivity and that geometric effects that stabilize CH 2 CH 2 * compared to CH 3 CH* are desirable properties of a better catalyst. Removing reactive bridge and 3-fold sites facilitates this, which may be achievable by sufficient concentrations of tin in platinum. The included model code furthermore provides a base for easy tuning and for expanding the study to other thermodynamic conditions, other facets, alloys or the reaction network to longer hydrocarbons or to oxidative pathways.</p> </div> </div>

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