Complex Chemical System Research Articles

A probabilistic framework for identifying biosignatures using Pathway Complexity.

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes—whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call ‘Pathway Complexity’, that allows us not only to threshold the abiotic–biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive.This article is part of the themed issue ‘Reconceptualizing the origins of life’.

Toward Artificial Mitochondrion: Mimicking Oxidative Phosphorylation in Polymer and Hybrid Membranes.

For energy supply to biomimetic constructs, a complex chemical energy-driven ATP-generating artificial system was built. The system was assembled with bottom-up detergent-mediated reconstitution of an ATP synthase and a terminal oxidase into two types of novel nanocontainers, built from either graft copolymer membranes or from hybrid graft copolymer/lipid membranes. The versatility and biocompatibility of the proposed nanocontainers was demonstrated through convenient system assembly and through high retained activity of both membrane-embedded enzymes. In the future, the nanocontainers might be used as a platform for the functional reconstitution of other complex membrane proteins and could considerably expedite the design of nanoreactors, biosensors, and artificial organelles.

A Novel Encoded Recording Strategy of Complex Chemical System

Complex chemical system (CCS) is a complex mixture of systems, which is pervasive in nature. In this study, a novel encoded recording strategy of a CCS was proposed. The reaction medium for CCS was built using ink-jet printing technology and numerous information of the CCS was obtained using the technology of color reaction imaging. An imaging method, called chemical two-dimensional code (C2d) was established to express the information of CCS. This strategy can be used as a digital language (C2d) to improve the capabilities of exploring the relationships of CCS.

Modeling of ethylbenzene dehydrogenation kinetics process taking into account deactivation of catalyst bed of the reactor

Styrene synthesis process occurring in a two-stage continuous adiabatic reactor is a complex chemical engineering system. It is characterized by indeterminacy, nonstationarity and occurs in permanent uncontrolled disturbances. Therefore, the task of developing the predictive control system of the main product concentration of the dehydrogenation reaction - styrene to maintain this value within a predetermined range throughout the period of operation is important. This solution is impossible without the development of the process model on the basis of the kinetic revised scheme, taking into account the drop of the reactor catalytic bed activity due to coke formation on the surface. The article justifies and proposes: the drop changes dependence of catalyst bed activity as a time of reactor block operation function and improved model of chemical reactions kinetics. The synthesized mathematical model of the process is a system of ordinary differential equations and allows you: to calculate the concentration profiles of reaction mixture components during the passage of the charge through the adiabatic reactor stage, to determine the contact gas composition at the outlet of the reactor stages throughout the cycle of catalytic system, taking into account temperature changes and drop of the catalyst bed activity. The compensation of the decreased catalyst bed activity is carried out by raising the temperature in the reactor block for the duration of the operation. The estimation of the values of chemical reactions rate constants, as well as the calculation and analysis of the main and by-products concentrations of dehydrogenation reactions at the outlet of the reactor plant is curried out. Simulation results show that the change of temperature of the reactor, carried out by the exponential law considering deactivation of the catalyst bed allows the yield in a given range of technological regulations throughout the operation cycle of the reactor block.

Green enhanced oil recovery (GEOR)

Green enhanced oil recovery (GEOR) is a chemical enhanced oil recovery (EOR) method involving the injection of specific green chemicals (surfactants/alcohols/polymers) that effectively displace oil because of their phase-behaviour properties, which decrease the interfacial tension (IFT) between the displacing liquid and the oil. In this process, the primary displacing liquid slug is a complex chemical system called a micellar solution, containing green surfactants, co-surfactants, oil, electrolytes and water. The surfactant slug is relatively small, typically 10% pore volume (PV). It may be followed by a mobility buffer such as polymer. The total volume of the polymer solution is typically ~1 PV. This study was conducted to examine the effectiveness of the combination of microbial by-products Bacillus subtilise strain JF-2 bio-surfactant and alcohol in recovering residual oil. It also considered whether bio-surfactant capability could be improved by blending it with non-ionic green surfactant. The study consisted of a phase behaviour study, IFT measurement and core-flooding experiments. In the phase behaviour study, it was found that 0.5% alkyl polyglycosides (APG) and 0.5–1.00% of butanol at 2% NaCl gave stable middle phase micro-emulsion. Non-ionic (APG 264) and anionic (bio-surfactant) mixtures are able to form stable middle phase micro-emulsion. Based on IFT reduction, two low concentrations (40 and 60 mg/l) of JF-2 bio-surfactant were identified where IFT values were low. The bio-surfactant and butanol formulation produced a total ~39.3% of oil initially in place (OIIP).

Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory.

Gibbs' macroscopic chemical thermodynamics is one of the most important theories in chemistry. Generalizing it to mesoscaled nonequilibrium systems is essential to biophysics. The nonequilibrium stochastic thermodynamics of chemical reaction kinetics suggested a free energy balance equation dF^{(meso)}/dt=E_{in}-e_{p} in which the free energy input rate E_{in} and dissipation rate e_{p} are both non-negative, and E_{in}≤e_{p}. We prove that in the macroscopic limit by merely allowing the molecular numbers to be infinite, the generalized mesoscopic free energy F^{(meso)} converges to φ^{ss}, the large deviation rate function for the stationary distributions. This generalized macroscopic free energy φ^{ss} now satisfies a balance equation dφ^{ss}(x)/dt=cmf(x)-σ(x), in which x represents chemical concentration. The chemical motive force cmf(x) and entropy production rate σ(x) are both non-negative, and cmf(x)≤σ(x). The balance equation is valid generally in isothermal driven systems and is different from mechanical energy conservation and the first law; it is actually an unknown form of the second law. Consequences of the emergent thermodynamic quantities and equalities are further discussed. The emergent "law" is independent of underlying kinetic details. Our theory provides an example showing how a macroscopic law emerges from a level below.

Profiling of volatile organic compounds released from individual intact juvenile and mature citrus leaves

Plants release volatiles to communicate with each other and to attract or repel insects. The methods used to collect volatiles are varied. Here, we describe a simple solvent-less, solid phase microextraction-based method to collect the volatiles released from intact citrus leaves. We were able to collect up to 39 volatiles from both juvenile and mature leaves. Our results indicated that juvenile leaves produced both monoterpenes and sesquiterpenes, and while mature leaves continued to produce a variety of monoterpenes, their release of sesquiterpenes decreased dramatically. The finding that juvenile leaves emitted higher levels of sesquiterpenes while mature leaves released mostly monoterpenes suggests that younger leaves of plants may be involved in a more complex chemical communication system.

Multi-Scale Modeling of the Gamma Radiolysis of Nitrate Solutions.

A multiscale modeling approach has been developed for the extended time scale long-term radiolysis of aqueous systems. The approach uses a combination of stochastic track structure and track chemistry as well as deterministic homogeneous chemistry techniques and involves four key stages: radiation track structure simulation, the subsequent physicochemical processes, nonhomogeneous diffusion-reaction kinetic evolution, and homogeneous bulk chemistry modeling. The first three components model the physical and chemical evolution of an isolated radiation chemical track and provide radiolysis yields, within the extremely low dose isolated track paradigm, as the input parameters for a bulk deterministic chemistry model. This approach to radiation chemical modeling has been tested by comparison with the experimentally observed yield of nitrite from the gamma radiolysis of sodium nitrate solutions. This is a complex radiation chemical system which is strongly dependent on secondary reaction processes. The concentration of nitrite is not just dependent upon the evolution of radiation track chemistry and the scavenging of the hydrated electron and its precursors but also on the subsequent reactions of the products of these scavenging reactions with other water radiolysis products. Without the inclusion of intratrack chemistry, the deterministic component of the multiscale model is unable to correctly predict experimental data, highlighting the importance of intratrack radiation chemistry in the chemical evolution of the irradiated system.

A network pharmacology approach to discover active compounds and action mechanisms of San-Cao Granule for treatment of liver fibrosis.

Ethnopharmacological relevanceSan-Cao Granule (SCG) has been used in patients with liver fibrosis for many years and has shown good effect. However, its mechanism of therapeutic action is not clear because of its complex chemical system. The purpose of our study is to establish a comprehensive and systemic method that can predict the mechanism of action of SCG in antihepatic fibrosis.Materials and methodsIn this study, a “compound–target–disease” network was constructed by combining the SCG-specific and liver fibrosis–specific target proteins with protein–protein interactions, and network pharmacology was used to screen out the underlying targets and mechanisms of SCG for treatment of liver fibrosis. Then, some key molecules of the enriched pathway were chosen to verify the effects of SCG on liver fibrosis induced by thioacetamide (TAA).ResultsThis systematic approach had successfully revealed that 16 targets related to 11 SCG compounds were closely associated with liver fibrosis therapy. The pathway-enrichment analysis of them showed that the TGF-β1/Smad signaling pathway is relatively important. Animal experiments also proved that SCG could significantly ameliorate liver fibrosis by inhibiting the TGF-β1/Smad pathway.ConclusionSCG could alleviate liver fibrosis through the molecular mechanisms predicted by network pharmacology. Furthermore, network pharmacology could provide deep insight into the pharmacological mechanisms of Chinese herbal formulas.

Optimal Multiperiodic Control for Inventory Coupled Systems: A Multifrequency Second-Order Test

A complex autonomous inventory coupled system is considered. It can take, for example, the form of a network of chemical or biochemical reactors, where the inventory interactions perform the recycling of by-products between the subsystems. Because of the flexible subsystems interactions, each of them can be operated with their own periods utilizing advantageously their dynamic properties. A multifrequency second-order test generalizing the p-test for single systems is described. It can be used to decide which kind of the operation (the static one, the periodic one or the multiperiodic one) will intensify the productivity of a complex system. An illustrative example of the multiperiodic optimization of a complex chemical production system is presented.

Multi-constituent determination and fingerprint analysis of Scutellaria indica L. using ultra high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry.

An ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry method integrating multi-constituent determination and fingerprint analysis has been established for quality assessment and control of Scutellaria indica L. The optimized method possesses the advantages of speediness, efficiency, and allows multi-constituents determination and fingerprint analysis in one chromatographic run within 11 min. 36 compounds were detected, and 23 of them were unequivocally identified or tentatively assigned. The established fingerprint method was applied to the analysis of ten S. indica samples from different geographic locations. The quality assessment was achieved by using principal component analysis. The proposed method is useful and reliable for the characterization of multi-constituents in a complex chemical system and the overall quality assessment of S. indica.

Experimentally determined distribution of fluorine and chlorine upon hydrous slab melting, and implications for F–Cl cycling through subduction zones

Fluorine and chlorine are volatile elements known to be enriched in primitive arc magmas, and variations of F/Cl ratios can carry information about slab devolatilization processes. Recent experiments on the fractionations of these elements suggest that aqueous fluid has limited capacity to enrich the magma source region in F. Hence, it is difficult to explain observations of primitive arc magmas particularly rich in F. To complement previous experimental studies, we examined the fractionation of fluorine and chlorine during hydrous partial melting of subducting slab. Element-doped phase equilibria experiments were carried out in a complex chemical system at conditions equivalent to potential slab melting temperatures (750–1000°C) across the amphibolite to eclogite facies transition (1.3–3GPa). Partition coefficients of F and Cl between hydrous silicic melts and minerals were determined by electron microprobe and/or ion probe. Fluorine is compatible in amphibole (DFamp/glass=1.18–1.85), and incompatible in garnet (0.034–0.140), clinopyroxene (0.059–0.505), and allanite (0.205–0.504). Hence, amphibole is an important F host, and can retain significant quantities of F in the solid residue of partial melting. On the contrary, Cl is incompatible, with DClmineral/glass generally decreasing from amphibole (0.079–0.625; one outlier at 1.87) to allanite (0.163), clinopyroxene (0.066–0.158), and garnet (0.031–0.153; outlier at 0.492). As a result, Cl is easily mobilized during partial melting. Fluorine and chlorine release during slab melting have been quantified by applying our partition coefficients to a non-modal batch melting model. The model shows that amphibole plays a key role in F/Cl fractionation during partial melting, while F/Cl is close to that of source for the melting of amphibole free eclogite. Moreover, the results from a flux-melting model employing several source compositions are compared to F and Cl abundances in primitive arc magmas. The observed variations are best described by variable additions of slab-derived aqueous fluids and hydrous melts to the mantle wedge melting region.

Coexistence of activator and inhibitor for Brusselator diffusion system in chemical or biochemical reactions

In this paper, we consider a reaction–diffusion system known as the Brusselator model with homogenous Neumann boundary conditions. The model is a system of two differential equations which describes a type of complex chemical or biochemical reaction system. We mainly study the coexistence of non-constant positive solutions to the model.

Kinetics and mechanism of homogeneous oxidative dehydrogenation of cyclohexane with nitrous oxide

The most probable mechanism of the coherently synchronized oxidative dehydrogenation of cyclohexane and decomposition of nitrous oxide was suggested. A kinetic model, which adequately describes the experimental data, was developed on the basis of this mechanism and used to calculate the kinetic parameters of this complex chemical system.

Photoactivated biological processes as quantum measurements.

We outline a framework for describing photoactivated biological reactions as generalized quantum measurements of external fields, for which the biological system takes on the role of a quantum meter. By using general arguments regarding the Hamiltonian that describes the measurement interaction, we identify the cases where it is essential for a complex chemical or biological system to exhibit nonequilibrium quantum coherent dynamics in order to achieve the requisite functionality. We illustrate the analysis by considering measurement of the solar radiation field in photosynthesis and measurement of the earth's magnetic field in avian magnetoreception.

Identification and quantitative characterization of PSORI-CM01, a Chinese medicine formula for psoriasis therapy, by liquid chromatography coupled with an LTQ Orbitrap mass spectrometer.

PSORI-CM01 is a Chinese medicine formula prepared from medicinal herbs and used in China for the treatment of psoriasis. However, the chemical constituents in PSORI-CM01 have not been clarified yet. In order to quickly define the chemical profiles and control the quality of PSORI-CM01 preparations, ultra-high liquid chromatography coupled with electrospray ionization hybrid linear trap quadrupole Orbitrap mass spectrometry (UHPLC-ESI-LTQ/Orbitrap-MS) was applied for simultaneous identification and quantification of multiple constituents. A total of 108 compounds, including organic acids, phenolic acids, flavonoids, and terpenoids, were identified or tentatively deduced on the base of their retention behaviors, MS and MSn data, or by comparing with reference substances and literature data. In addition, an optimized UHPLC-ESI-MS method was established for the quantitative determination of 14 marker compounds in different dosage forms of PSORI-CM01 preparations. The validation of the method, including spike recoveries, linearity, sensitivity (LOQ), precision, and repeatability, was carried out and demonstrated to be satisfied the requirements of quantitative analysis. This is the first report on the comprehensive determination of chemical constituents in PSORI-CM01 preparations by UHPLC-ESI-LTQ/Orbitrap mass spectrometry. The results suggested that the established methods would be a powerful and reliable analytical tool for the characterization of multi-constituents in complex chemical system and quality control of TCM preparations.

Predicting kinetic dependences and closing the balance: Wei and Prater revisited

The chemical system of monomolecular reactions among n species, first analysed in the classical paper by Wei and Prater (1962) was revisited. It was shown that using symmetry relationships, based on all the equilibrium constants and n(n−1)/2 known dependences, all remaining kinetic dependences can be calculated. A new method of closing the mass balance for such a complex chemical system was developed, using only measurements of one or a few species, and based on symmetry relations. A new method of testing completeness of a kinetic description was proposed, using the properties of the trace sum of components, i.e., the sum of all concentration dependences, each of which is started from maximal initial concentration.

Variant and invariant states for chemical reaction systems

Models of chemical reaction systems can be quite complex as they typically include information regarding the reactions, the inlet and outlet flows, the transfer of species between phases and the transfer of heat. This paper builds on the concept of reaction variants/invariants and proposes a linear transformation that allows viewing a complex nonlinear chemical reaction system via decoupled dynamic variables, each one associated with a particular phenomenon such as a single chemical reaction, a specific mass transfer or heat transfer. Three aspects are discussed, namely, (i) the decoupling of reactions and transport phenomena in open non-isothermal both homogeneous and heterogeneous reactors, (ii) the decoupling of spatially distributed reaction systems such as tubular reactors, and (iii) the potential use of the decoupling transformation for the analysis of complex reaction systems, in particular in the absence of a kinetic model.

Qualitative and quantitative analysis of Rhizoma Smilacis glabrae by ultra high performance liquid chromatography coupled with LTQ OrbitrapXL hybrid mass spectrometry.

Rhizoma Smilacis glabrae, a traditional Chinese medicine (TCM) as well as a functional food, has been commonly used for detoxification treatments, relieving dampness and as a diuretic. In order to quickly define the chemical profiles and control the quality of Smilacis glabrae, ultra high performance liquid chromatography coupled with electrospray ionization hybrid linear trap quadrupole orbitrap mass spectrometry (UHPLC-ESI/LTQ-Orbitrap-MS) was applied for simultaneous identification and quantification of its bioactive constituents. A total of 56 compounds, including six new compounds, were identified or tentatively deduced on the basis of their retention behaviors, mass spectra, or by comparison with reference substances and literature data. The identified compounds belonged to flavonoids, phenolic acids and phenylpropanoid glycosides. In addition, an optimized UHPLC-ESI/LTQ-Orbitrap-MS method was established for quantitative determination of six marker compounds from five batches. The validation of the method, including linearity, sensitivity (LOQ), precision, repeatability and spike recoveries, was carried out and demonstrated to be satisfied the requirements of quantitative analysis. The results suggested that the established method would be a powerful and reliable analytical tool for the characterization of multi-constituent in complex chemical system and quality control of TCM.

In Situ Investigation on Spatiotemporal Changes of SEI Properties By SECM

In our society Li-ion batteries are widely used, especially for small-scale devices. During the first charging process the solid-electrolyte-interface (SEI) between the electrode and electrolyte is established. This layer passivates the surface against electron transfer reaction but allows transfer of Li-ions. In order to realize high-energy Li-ion batteries in conventional carbonate-based electrolytes, the formation of the SEI is required.[1] Content and structure of the SEI are highly discussed.[2, 3] The SEI represents a complex chemical system, where several solid, liquid and gaseous compounds establish interdependent equilibria. Characterization of the SEI is a difficult challenge, because of the similar chemical identity of SEI components and electrolyte molecules. Furthermore, ex situ analysis of the SEI requires separation and isolation of the SEI, which may change the content and the structure of the SEI.[3] In situ analysis is highly sought after to circumvent this problem.In our approach we use the scanning electrochemical microscopy (SECM) to investigate in situ the electron transport across the SEI. For this purpose, a redox mediator is added to the electrolyte, which communicates between the battery electrode and the positionable ultra-microelectrode (UME). Our results by SECM demonstrate the dynamic of SEI formation and dissolution. Furthermore, the swelling behavior of practical graphite anodes in standard battery electrolytes is characterized.