Enhancement of Prebiotic Peptide Formation in Cyclic Environments.

Hamiltonian classical thermodynamics and chemical kinetics

The biochemical activation of amino acids by adenosine triphosphate (ATP) drives the synthesis of proteins that are essential for all life. On the early Earth, before the emergence of cellular life, the chemical condensation of amino acids to form prebiotic peptides or proteins may have been activated by inorganic polyphosphates, such as tri metaphosphate (TP). Plausible volcanic and other potential sources of TP are known, and TP readily activates amino acids for peptide synthesis. But de novo peptide synthesis also depends on pH, temperature, and processes of solvent drying, which together define a varied range of potential activating conditions. Although we cannot replay the tape of life on Earth, we can examine how activator, temperature, acidity and other conditions may have collectively shaped its prebiotic evolution. Here, reactions of two simple amino acids, glycine and alanine, were tested, with or without TP, over a wide range of temperature (0-100°C) and acidity (pH1-12), while open to the atmosphere. After 24h, products were analyzed by HPLC and mass spectrometry. In the absence of TP, glycine and alanine readily formed peptides under harsh near-boiling temperatures, extremes of pH, and within dry solid residues. In the presence of TP, however, peptides arose over a much wider range of conditions, including ambient temperature, neutral pH, and in water. These results show how polyphosphates such as TP may have enabled the transition of peptide synthesis from harsh to mild early Earth environments, setting the stage for the emergence of more complex prebiotic chemistries.

Several interrelated problems in connection with the treatment of sulfur dioxide at temperatures between 700 and 800°C were studied. The interaction of SO2 with Al2O3 was studied experimentally using B.E.T., thermogravimetry and temperature-programmed desorption. Adsorption takes place through a wide range of binding energies, with some SO2 adsorbing irreversibly at temperatures below 800°C. The amount adsorbed depends on the surface history and thermal treatment. An adsorption isotherm based on a bimodal energy distribution provides an adequate description of the equilibrium process. The chemical composition, sulfation and regeneration of an alkali-alumina sorbent for sulfur dioxide were studied using thermogravimetry, gas chromatography, and X-ray photoelectron spectroscopy. The active sorbent consists of a thin layer of sodium and lithium aluminates supported on alumina. The rate of sulfation is proportional to the SO2 concentration in the gas, up to [SO2] ≈ 5000 ppm. The activation energy of the sulfation is E = 21.6 kcal/mole. The sulfated sorbent was regenerated by reduction with CO at 700-800°C. Sulfur removal from the sorbent and distribution of gaseous products were measured at different alkali loadings, temperatures and CO concentrations. The reduction takes place in two consecutive stages through a complex reaction network in which the alumina support plays a decisive role, both as a reactant and as a catalyst. A simplified reaction network is used as a basis for a kinetic model that provides an adequate description of the reduction process at moderate sorbent loadings.

Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate-thioester exchange, thiolate-disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov-Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving chemical systems.

Simulation of xanthan gum production by a chemically structured kinetic model

In biological networks, any manifestations of behaviors substantially 'deviant' from the predictions of continuous-deterministic classical chemical kinetics (CCK) are typically ascribed to systems with complex dynamics and/or a small number of molecules. Here we show that in certain cases such restrictions are not obligatory for CCK to be largely incorrect. By systematically identifying properties that may cause significant divergences between CCK and the more accurate discrete-stochastic chemical master equation (CME) system descriptions, we comprehensively characterize potential CCK failure patterns in biological settings, including consequences of the assertion that CCK is closer to the 'mode' rather than the 'average' of stochastic reaction dynamics, as generally perceived. We demonstrate that mechanisms underlying such nonclassical effects can be very simple, are common in cellular networks and result in often unintuitive system behaviors. This highlights the importance of deviant effects in biotechnologically or biomedically relevant applications, and suggests some approaches to diagnosing them in situ.

An electrochemical impedance study on atmospheric corrosion of steels in a cyclic wet-dry condition

This research focuses on influence of pore structure on chloride distribution in surface layer of cement paste under cyclic wet-dry condition. The results of chloride distribution reveal that drying and wetting cycles can lead to a peak value of chloride content (Cmax) occurring in surface layer of cement paste. Cmax increases with the increase of W/C. While the depth (Δx) at which Cmax appears does not show a regular change. Moreover, Cmax should be used to predict service life of concrete structures when Cmax appears in the chloride profiles. For the influence of pore structure, there exists an obvious hyperbolic relationship between chloride diffusion coefficient (D), Cmax and pore structure parameters. D and Cmax increase with total porosity and the most probable pore diameter, decrease with tortuosity, and stabilize gradually. And the most probable pore diameter has the most significant impact on D and Cmax. In addition, XRD and SEM-EDS results indicate that the deposition of Friedel’s salt results in the formation of more inkbottle shaped pores, which may cause the appearance of Cmax under cyclic drying-wetting conditions due to hysteretic moisture effect.

Introduction: Construction joint is common and even inevitable in most of the reinforcement concrete structures. This study was to assess the effect of construction joints on chloride-induced corrosion of reinforcing steel in concrete.Methods: Test parameters included two environmental conditions (salt solution immersion condition and cyclic wet-dry condition), two forms of construction joint (direct wet joint and roughened wet joint) and four types of steel bar (mild steel bar, ferritic stainless-steel bar, austenitic-ferritic stainless-steel bar and epoxy-coated steel bar). The corrosion test of 90 specimens was carried out by electrochemical accelerated corrosion method. The weight loss of each steel bar and steel bar section in specimens was measured. An influence coefficient (k_j) of construction joint on local weigh loss of steel bars was defined.Results: Except for epoxy-coated steel bars, the most severe corrosion of experimental steel bars in concrete specimens all occurred at the joints, while the corrosion in non-joint sections of steel bars was relatively uniform and less. The weight loss rate of specimens has the range of 1.18% to 15.73% with an average value of 6.22%. The average k_j of mild steel bars, S11203 stainless steel bars, and S23043 stainless steel bars are 1.38, 1.92, and 1.97, respectively. The average k_j of specimens in immersion condition and cyclic wet-dry condition are 1.44 and 2.07. The corrosion of epoxy-coated steel bars mainly occurred at the damage locations of epoxy coating, not mainly at the joints.Conclusion: Chloride-induced corrosion of steel bars at construction joints was always more severe than at non-joints, especially in cyclic wet-dry environments, even for stainless-steel bar, but epoxy-coated steel bars were excluded.

Role of hygroscopic chloride salts on corrosion performance and hydrogen absorption of steel under cyclic wet-dry conditions

Insight into the corrosion evolution of Fe-based amorphous coatings under wet-dry cyclic conditions

Over 150 mutations in SOD1 (superoxide dismutase-1) cause amyotrophic lateral sclerosis (ALS), presumably by accelerating SOD1 amyloidogenesis. Like many nucleation processes, SOD1 fibrillization is stochastic (in vitro), which inhibits the determination of aggregation rates (and obscures whether rates correlate with patient phenotypes). Here, we diverged from classical chemical kinetics and used Kaplan-Meier estimators to quantify the probability of apo-SOD1 fibrillization (in vitro) from ∼103 replicate amyloid assays of wild-type (WT) SOD1 and nine ALS variants. The probability of apo-SOD1 fibrillization (expressed as a Hazard ratio) is increased by certain ALS-linked SOD1 mutations but is decreased or remains unchanged by other mutations. Despite this diversity, Hazard ratios of fibrillization correlated linearly with (and for three mutants, approximately equaled) Hazard ratios of patient survival (R2 = 0.67; Pearson's r = 0.82). No correlation exists between Hazard ratios of fibrillization and age of initial onset of ALS (R2 = 0.09). Thus, Hazard ratios of fibrillization might explain rates of disease progression but not onset. Classical kinetic metrics of fibrillization, i.e., mean lag time and propagation rate, did not correlate as strongly with phenotype (and ALS mutations did not uniformly accelerate mean rate of nucleation or propagation). A strong correlation was found, however, between mean ThT fluorescence at lag time and patient survival (R2 = 0.93); oligomers of SOD1 with weaker fluorescence correlated with shorter survival. This study suggests that SOD1 mutations trigger ALS by altering a property of SOD1 or its oligomers other than the intrinsic rate of amyloid nucleation (e.g., oligomer stability; rates of intercellular propagation; affinity for membrane surfaces; and maturation rate).

The initial nucleation and growth of atomic layer deposited HfO2 films under various surface conditions were investigated by in situ medium energy ion scattering analysis. The influences of an O–H terminated surface on the initial growth stage were investigated in detail using the atomic density of Hf that reacted on the surface. The measured growth rate of HfO2 per cycle was applied to a mathematical model based on classical chemical kinetics. A parabolic initial growth with an extremely low rate at the initial stage of growth was observed for the film with a hydrogen-terminated surface. However, linear growth, with a value of 1.41×1014Hfatoms∕cm2cycle, was maintained for films grown on an O–H terminated surface. The ∼1∕6 steric hindrance factor extracted from a phenomenological model was related to the size of the tetrahedral HfCl4 molecule and the possible attachment sites. Moreover, the surface roughness and electrical properties of the atomic layer deposited HfO2 films show a strong dependence on the initial nucleation and growth on the different surface conditions.

Modelling the pyrolysis of tar sands in fluidized bed reactors

Fundamental kinetics model of acidity-activity relation for ethylene oligomerization and aromatization over ZSM-5 zeolites