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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS2022

The hierarchical organization of autocatalytic reaction networks and its relevance to origin of life

Abiogenesis has long been suspected to require that chemical reaction networks contain multiple autocatalytic cores, but little is known about what features of these networks allow for the gradual accretion of complexity. To identify realistic scenarios for the emergence of life-like properties, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical “seeds”. We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks and biological ecosystems. Applying our algorithms to both an abiotic reaction network and a biochemical one, each driven by a set of simple food chemicals, we detect SDASs that are organized as trophic tiers, of which the higher tier can be seeded by relatively simple chemicals if the lower tier is already activated. This indicates that sequential activation of trophically organized SDASs by seed chemicals that are not much more complex than what already exist could be a mechanism of gradual complexification from relatively simple abiotic reactions to more complex life-like systems. Interestingly, in both reaction networks, higher-tier SDASs include chemicals that might alter emergent features of chemical systems and could serve as early targets of selection. Our analysis provides computational tools for analyzing very large chemical/biochemical reaction networks and suggests new approaches to studying abiogenesis in the lab.

Zhen Peng↗
NASA NTRS2019

Finding Evidence of a Prebiotic Pyruvate Reaction Network in Meteorites

The organic compounds of carbonaceous chondrites are structurally diverse products of the prolonged abiotic chemistry that occurred before and during the early stages of the solar system. They also represent the types of prebiotic compounds that may have participated in chemical evolutionary processes that gave rise to life. Pyruvic acid is a key component of primary metabolism that has recently been found in carbonaceous chondrites. Its prominence in biology has inspired us to explore its chemistry and possible role in the origin of metabolism. Our laboratory investigations have found that pyruvate (the ionized form of pyruvic acid) can serve as a single-source reactant to generate what we term a pyruvate reaction network (PRN). The core of the PRN is driven by pyruvate aldol polymerization and decay reactions. These decay reactions lead to the production of stable and unstable compounds which include mono, di, and tricarboxylic acids and a variety of keto acids. Importantly, many of these reactions apparently lead back to pyruvate, establishing a feedback process. Finding evidence of this reaction network in meteorites would establish that the chemistry of pyruvate did occur in a prebiotic environment and indeed many of the known compounds found in pyruvate reaction mixtures were detected in the Murchison and Murray meteorites. However, multiple synthetic origins, not tied to pyruvate chemistry, might also explain their meteoritic presence. Thus finding compounds unique to the PRN, such as reaction intermediates, would provide stronger evidence in support of its prebiotic relevance. The identity of these intermediates can only be con-firmed by acquiring chemical standards, however, as most are not available commercially, we engaged in extensive chemical synthesis. Obtaining these standards also provides the opportunity to study their subsequent chemistry and roles in the PRN.

Rios, A. C.↗
NASA NTRS2019

Finding Evidence of a Prebiotic Pyruvate Reaction Network in Meteorites

The organic compounds of carbonaceous chondrites are structurally diverse products of the prolonged abiotic chemistry that occurred before and during the early stages of the solar system. They also represent the types of prebiotic compounds that may have participated in chemical evolutionary processes that gave rise to life. Pyruvic acid is a key component of primary metabolism that has recently been found in carbonaceous chondrites. Its prominence in biology has inspired us to explore its chemistry and possible role in the origin of metabolism. Our laboratory investigations have found that pyruvate (the ionized form of pyruvic acid) can serve as a single-source reactant to generate what we term a pyruvate reaction network (PRN). The core of the PRN is driven by pyruvate aldol polymerization and decay reactions. These decay reactions lead to the production of stable and unstable compounds which include mono, di, and tricarboxylic acids and a variety of keto acids. Importantly, many of these reactions apparently lead back to pyruvate, establishing a feedback process. Finding evidence of this reaction network in meteorites would establish that the chemistry of pyruvate did occur in a prebiotic environment and indeed many of the known compounds found in pyruvate reaction mixtures were detected in the Murchison and Murray meteorites. However, multiple synthetic origins, not tied to pyruvate chemistry, might also explain their meteoritic presence. Thus finding compounds unique to the PRN, such as reaction intermediates, would provide stronger evidence in support of its prebiotic relevance. The identity of these intermediates can only be confirmed by acquiring chemical standards, however, as most are not available commercially, we engaged in extensive chemical synthesis. Obtaining these standards also provides the opportunity to study their subsequent chemistry and roles in the PRN.

Rios, Andro↗
NASA NTRS2019

Synthesis of Meteoritic Reaction Intermediates

The organic compounds of carbo- naceous chondrites are structurally diverse products of the prolonged abiotic chemistry that occurred before and during the early stages of the solar system [1]. They also represent the types of prebiotic compounds that may have participated in chemical evolutionary processes that gave rise to life [2]. Pyruvic acid is a key component of primary metabolism that has recently been found in carbonaceous chondrites [3]. Its prominence in biology has inspired us to explore its chemistry and possible role in the origin of metabolism. Our laboratory investigations have found that pyruvate (the ionized form of pyruvic acid) can serve as a single-source reactant to generate what we term a pyruvate reaction network (PRN). The core of the PRN is driven by pyruvate aldol polymerization and decay reactions. These decay reactions lead to the production of stable and unstable compounds which include mono, di, and tricarboxylic acids and a variety of keto acids. Finding evidence of this reaction network in meteorites would establish that the chemistry of pyruvate did occur in a prebiotic environment. Many of the known compounds found in pyruvate reaction mixtures were originally detected in meteorite samples by Cooper et al in 2011. However, multiple synthetic origins not tied to pyruvate chemistry might also explain their meteoritic presence. Thus, a search to find compounds unique to the PRN, such as reaction intermediates, would provide stronger evidence to demonstrate its prebiotic relevance. The identity of these intermediates can only be confirmed by acquiring chemical standards, however, as most are not available commercially, they need to be accessed through chemical synthesis.

Rios, Andro C.↗
NASA NTRS1980

The chemical abundances of the Cassiopeia A fast-moving knots - Explosive nucleosynthesis on a minicomputer

A simplified nuclear reaction network for explosive nucleosynthesis calculations is described in which only the most abundant nuclear species and the most important reactions linking these species are considered. This scheme permits the exploration of many cases without excessive computational effort. Good agreement with previous calculations employing more complex reaction networks is obtained. This scheme is applied to the observed chemical abundances of the fast-moving knots in the supernova remnant Cassiopeia A and it is found that a wide range of initial conditions could yield the observed abundances. The abundances of four of the knots with significant and different amounts of elements heavier than oxygen are consistent with an origin in material of the same initial composition but processed at different peak temperatures and densities. Despite the observed high oxygen abundances and low abundances of light elements in the knots, they did not necessarily undergo incomplete oxygen burning; in fact, it is not even necessary that oxygen have been present in the initial composition. The agreement between the calculated and observed chemical abundances in Cas A and similar supernova remnants depends primarily upon the relevant nuclear physics and does not provide strong evidence in favor of any particular model of the supernova event.

Johnston, M. D.↗
NASA NTRS1984

The CN radical in diffuse interstellar clouds

A survey of 15 lines of sight for the CN B2Sigma(+) X2Sigma(+) interstellar absorption lines shows that the CN column density in diffuse interstellar clouds follows the relation log N(CN) is proportional to m log N(H2), where m is approximately equal to 3. This result is reproduced by a reaction network in which CN is produced primarily from C2 by the neutral-neutral reaction C2 + N yields CN + C, and photodissociation is the main destruction pathway for the neutral molecules CH, C2, and CN. The CN radical is the first molecular species observed in diffuse clouds that requires a neutral-neutral reaction for its formation in the gas phase. The network also reproduces the observed ratio N(CN)/N(H2).

Federman, S. R.↗
NASA NTRS2001

Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

Beard, Daniel A.↗
NASA NTRS1980

A model of comet comae. II - Effects of solar photodissociative ionization

Improvements to a computer model of coma photochemistry are described. These include an expansion of the chemical reactions network and new rate constants that have been measured only recently. Photolytic reactions of additional molecules are incorporated, and photolytic branching ratios are treated in far greater detail than previously. A total of 25 photodissociative ionization (PDI) reactions are now considered (as compared to only 3 PDI reactions previously). Solar PDI of the mother molecule CO2 is shown to compete effectively with photoionization of CO in the production of observed CO(+). The CO(+) density peak predicted by the improved model, for CO2 or CO mother molecules, is deep in the inner coma, in better agreement with observation than the old CO2 model. However, neither CO2 nor CO mother molecule calculations reproduce the CO(+)/H2O(+) ratio observed in comet Kohoutek. PDI products of CO2, CO, CH4, and NH3 mother molecules fuel a complex chemistry scheme, producing inner coma abundances of CN, C2, and C3 much greater than previously calculated.

Huebner, W. F.↗
NASA NTRS2001

Delivering Faster Congestion Feedback with the Mark-Front Strategy

Computer networks use congestion feedback from the routers and destinations to control the transmission load. Delivering timely congestion feedback is essential to the performance of networks. Reaction to the congestion can be more effective if faster feedback is provided. Current TCP/IP networks use timeout, duplicate Acknowledgement Packets (ACKs) and explicit congestion notification (ECN) to deliver the congestion feedback, each provides a faster feedback than the previous method. In this paper, we propose a markfront strategy that delivers an even faster congestion feedback. With analytical and simulation results, we show that mark-front strategy reduces buffer size requirement, improves link efficiency and provides better fairness among users. Keywords: Explicit Congestion Notification, mark-front, congestion control, buffer size requirement, fairness.

Liu, Chunlei↗
NASA NTRS1993

Primordial nucleosynthesis and the abundances of beryllium and boron

The recently attained ability to make measurements of Be and B as well as to put constraints on Li-6 abundances in metal-poor stars has led to a detailed reexamination of big bang nucleosynthesis in the A is greater than about 6 regime. The nuclear reaction network has been significantly expanded, with many new rates added. It is demonstrated that although a number of A is greater than 7 reaction rates are poorly determined, even with extreme values chosen, the standard homogeneous model is unable to produce significant yields above A = 7, and the (Li-7)/(Li-6) ratio always exceeds 500. We also preliminarily explore inhomogeneous models, such as those inspired by a first-order quark-hadron phase transition, where regions with high neutron/proton ratios can allow some leakage up to A is greater than 7. However, models that fit the A is not greater than 7 abundances still seem to have difficulty in obtaining significant A is greater than 7 yields.

Thomas, David↗
NASA NTRS2021

Neutral–neutral synthesis of organic molecules in cometary comae

Remote and in situ observations of cometary gases have revealed the presence of a wealth of complex organic molecules, including carbon chains, alcohols, imines, and the amino acid glycine. Such chemical complexity in cometary material implies that impacts by comets could have supplied reagents for prebiotic chemistry to young planetary surfaces. However, the assumption that some of the molecules observed in cometary comae at millimetre wavelengths originate from ices stored inside the nucleus has not yet been proven. In fact, the comae of moderately-active comets reach sufficient densities within a few thousand kilometres of the nucleus for an active (solar radiation-driven) photochemistry to ensue. Here, we present results from our latest chemical-hydrodynamic models incorporating an updated reaction network, and show that the commonly-observed HC3N (cyanoacetylene) and NH2CHO (formamide) molecules can be efficiently produced in cometary comae as a result of two-body, neutral–neutral, gas-phase reactions involving well-known coma species. In the presence of a near-nucleus distributed source of CN (similar to that observed by the Rosetta spacecraft at comet 67P), we find that sufficient HC3N and NH2CHO can be synthesized to match the abundances of these molecules observed previously in Oort cloud comets. The precise coma origins of these (and other) complex organic molecules can be verified through radio interferometric mapping observations, for example using the Atacama Large Millimeter/submillimeter Array.

Comets↗
NASA NTRS1987

Chemical network problems solved on NASA/Goddard's massively parallel processor computer

The single instruction stream, multiple data stream Massively Parallel Processor (MPP) unit consists of 16,384 bit serial arithmetic processors configured as a 128 x 128 array whose speed can exceed that of current supercomputers (Cyber 205). The applicability of the MPP for solving reaction network problems is presented and discussed, including the mapping of the calculation to the architecture, and CPU timing comparisons.

Cho, Seog Y.↗
NASA NTRS1997

Genetic Algorithm Approaches to Prebiobiotic Chemistry Modeling

We model an artificial chemistry comprised of interacting polymers by specifying two initial conditions: a distribution of polymers and a fixed set of reversible catalytic reactions. A genetic algorithm is used to find a set of reactions that exhibit a desired dynamical behavior. Such a technique is useful because it allows an investigator to determine whether a specific pattern of dynamics can be produced, and if it can, the reaction network found can be then analyzed. We present our results in the context of studying simplified chemical dynamics in theorized protocells - hypothesized precursors of the first living organisms. Our results show that given a small sample of plausible protocell reaction dynamics, catalytic reaction sets can be found. We present cases where this is not possible and also analyze the evolved reaction sets.

Lohn, Jason↗
NASA NTRS1972

CNO abundances and hydrodynamic models of the nova outburst.

We have used a fully implicit, Lagrangian, hydrodynamic computer code incorporating a nuclear reaction network to follow thermonuclear runaways in the hydrogen-rich envelopes of white dwarfs in order to produce a nova outburst. Because of the short time-scales and the high nuclear burning rates produced in our models, the nuclear reactions are far out of equilibrium and the beta-plus unstable nuclei become the most abundant nuclei in the envelope except for hydrogen and helium. Our models have ejected 1.00017 solar mass with kinetic energies of 8 times 10 to the 44-th power ergs, a value that agrees quite closely with the observed values for novae.

Starrfield, S.↗
NASA NTRS2000

The origin of intermediary metabolism

The core of intermediary metabolism in autotrophs is the citric acid cycle. In a certain group of chemoautotrophs, the reductive citric acid cycle is an engine of synthesis, taking in CO(2) and synthesizing the molecules of the cycle. We have examined the chemistry of a model system of C, H, and O that starts with carbon dioxide and reductants and uses redox couples as the energy source. To inquire into the reaction networks that might emerge, we start with the largest available database of organic molecules, Beilstein on-line, and prune by a set of physical and chemical constraints applicable to the model system. From the 3.5 million entries in Beilstein we emerge with 153 molecules that contain all 11 members of the reductive citric acid cycle. A small number of selection rules generates a very constrained subset, suggesting that this is the type of reaction model that will prove useful in the study of biogenesis. The model indicates that the metabolism shown in the universal chart of pathways may be central to the origin of life, is emergent from organic chemistry, and may be unique.

Non-NASA Center↗