Linear Chain Research Articles

Jump around: Selecting Markov Chain Monte Carlo parameters and diagnostics for improved food web model quality and ecosystem representation

Capturing ecological data variability in food web models is an important step for improving model representation of empirical systems. One approach is to use linear inverse modelling and Markov Chain Monte Carlo (LIM-MCMC) techniques to set up an inverse LIM problem using empirical data constraints, and then sample multiple plausible food webs from the inverse problem using an MCMC algorithm. We describe the set of plausible food webs as an ‘ensemble’ of solutions to the inverse problem sampled with the LIM-MCMC algorithm. The extent of data variability eventually integrated into an ensemble depends on how well the LIM-MCMC algorithm samples the solution space. Algorithm quality can be adjusted via user-defined parameters describing starting points, jump sizes, and number of iterations or food webs produced. However, little information exists on how each LIM-MCMC algorithm parameter affects the degree of empirical data variability introduced into the ensemble. Further, post hoc algorithm quality diagnostics with commonly used trace plots and the coefficient of variation (CoV) rarely address critical aspects of algorithm quality, such as (1) if the returned ensemble successfully targeted the solution space distribution (stationarity), (2) correlation between ensemble solutions (mixing), and (3) if the ensemble contains enough solutions to adequately capture input data variability (sampling efficiency). Therefore, we used several established MCMC convergence diagnostics to (1) quantify how algorithm parameters affect ensemble flow values and if these differences propagate to ecological indicators and (2) evaluate algorithm quality and compare to current evaluation and ecosystem modelling methods. We applied 30 LIM-MCMC algorithm combinations of varying starting points, jump sizes, and number of iterations to solve food web ensembles from a single food web model. We analysed ensembles with Ecological Network Analysis (ENA) to calculate indicators describing system function. Results show that LIM-MCMC algorithm parameters, in particular the jump size, affect ensemble flow values, which propagate to ecological indicators describing different ecosystem function of the same model. Thereafter, comparisons of post hoc diagnostics show that MCMC convergence diagnostics provided more robust estimates of algorithm quality than trace plots and CoV. Together, these findings underpin several novel recommendations to enhance LIM-MCMC algorithm parameter selection and quality assessments applicable to any ecological ensemble network study.

Attenuation of Lamb waves in coupled-resonator viscoelastic waveguide

Guidance of elastic waves is one of the main applications of artificial crystal structures. The attenuation of the guided waves is, however, often overlooked, as most of the proposed waveguides only comprise ideal elastic materials. In this work, we study the propagation of evanescent Lamb waves guided in coupled-resonator viscoelastic waveguide (CRVW), with special attention to attenuation. CRVW is defined by considering a linear chain of coupled defect cavities in a phononic plate made of epoxy. The viscoelastic behavior of epoxy is characterized numerically by the Kelvin–Voigt (K–V) model. Based on finite element analysis, the complex band structure and the spectrum of frequency response function (FRF) are obtained. Due to viscosity, guided Lamb waves are spatially damped. Two theoretical models are devised to predict the displacement distributions inside and outside a bandgap for guided waves, respectively, considering either the first or the first two least evanescent Bloch waves identified in the complex band structure. A CRVW sample is fabricated and characterized experimentally by laser vibrometry. Evanescent Lamb waves are observed to be strongly confined along the waveguide and at the same time to decay rapidly along the waveguide axis. Experiments and numerical simulations are found to be in fair agreement. The present work is expected to inspire practical applications of highly confined viscoelastic phononic waveguides.

Harmonic chain driven by active Rubin bath: transport properties and steady-state correlations

Characterizing the properties of an extended system driven by active reservoirs is a question of increasing importance. Here, we address this question in two steps. We start by investigating the dynamics of a probe particle connected to an ‘active Rubin bath’: a linear chain of overdamped run-and-tumble particles. We derive exact analytical expressions for the effective noise and dissipation kernels, acting on the probe and show that the active nature of the bath leads to a modified fluctuation–dissipation relation. In the next step, we study the properties of an activity-driven system, modelled by a chain of harmonic oscillators connected to two such active reservoirs at the two ends. We show that the system reaches a non-equilibrium stationary state (NESS), remarkably different from that generated due to a thermal gradient. We characterize this NESS by computing the kinetic temperature profile, spatial and temporal velocity correlations of the oscillators, and the average energy current flowing through the system. It turns out that the activity drive leads to the emergence of two characteristic length-scales, proportional to the activities of the reservoirs. Strong signatures of activity are also manifest in the anomalous short-time decay of the velocity autocorrelations. Finally, we find that the energy current shows a non-monotonic dependence on the activity drive and reversal in direction, corroborating previous findings.

An Integrated Circular Supply Chain Framework to Enhance Malaysian Business Performance

Businesses rely on supply chain management to suit the needs of global and multigenerational consumers. However, the current linear manufacturing and distribution supply chain strategy has been regarded as the source of dangerous waste generation, environmental deterioration, and the global warming phenomenon. In mitigating this issue, circular supply chain management, a practical integration model, is seen as the solution as it helps to reduce material flows and supply chain waste. Unfortunately, the fundamental mechanisms that can support its effective execution have not been comprehensively examined, hindering its complete incorporation into company strategy. Thus, to overcome this knowledge gap and improve organizational understanding, this study uses the systematic reviews and meta-analyses extension for scoping reviews (PRISMA-ScR) procedure to investigate the characteristics, enablers, and barriers of circular supply chain management. The study found five interconnected key structures: government, industry stakeholders, corporate management, end users, and financial institutions, all of which play important roles in the successful implementation of a circular supply chain strategy. As a result, close collaboration across the five identified stakeholders is essential to enable successful implementation. This study's objective is to the United Nations Sustainable Development Goals (SDGs) 8, 9, and 12, which aim to promote peace and prosperity for people and the planet both now and in the future.

Encapsulation of linear carbon chains in single-walled carbon nanotubes: Towards 1D van der Waals heterostructures for high-efficiency excitonic solar cells

One-dimensional van der Waals heterostructures (1D vdW HTs) based on single-walled carbon nanotubes (SWCNTs) encapsulating linear carbon chains (LCCs) with tunable optoelectronic properties provide a fresh ground for efficient excitonic solar cells (XSCs) alternative to those based on 2D monolayer materials. As an effort to identify for the first time 1D vdW HTs for efficient XSCs application, we perform here a systematic theoretical investigation on the energetic and structural stability, optoelectronic and photovoltaic properties of 1D vdW HTs based on SWCNTs encapsulating 50 symmetrical LCCs of different lengths, and capped with different conjugated endgroups through comprehensive first-principles calculations. We showed the fundamental role of the length and the endgroups effects in modulating the optoelectronic properties of LCCs. Through exploration of the energetic stability of the 1D vdW HTs of LCCs@SWCNTs from the universal force field (UFF) including vdW interactions, we determined the optimal SWCNTs diameters for which the resulting 1D vdW HTs are stable. Then, the band alignment in the 50 stable 1D vdW HTs of LCCs@SWCNTs is examined. Intriguingly, stable LCCs@SWCNTs are identified as type-II 1D vdW HTs complying the prerequisite of XSCs with strong optical absorption in the UV–visible-NIR spectral regions, and power conversion efficiency (PCE) reaching well over 21 %. These findings unravel the enormous potential of the 1D vdW HTs in designing next-generation XSCs devices competitive with state-of-the-art solar cells.

On Sombor index and graph energy of some chemically important graphs

Sombor index of a graph G=(V(G),E(G)) is provided by the expression ∑uv∈E(G)du2+dv2, where dx is the degree of the vertex x∈V(G). The energy of a graph is the quantity given by the total of the absolute values of its adjacency matrix’s eigenvalues. In this article, we improve the relation between the Sombor index and graph energy and derive the relation between them for unicyclic, bicyclic and tricyclic graphs, trees, triangular chain, square cactus chain and hexagonal cactus chain graphs. At last, we find the bounds of graph energy for zigzag and linear hexagonal chains.

Sliding on Slide-Ring Gels

Recent investigations have pointed to physical entanglements that greatly outnumber chemical crosslinks as key sources of energy dissipation and low friction in hydrogel networks. Slide-ring gels are an emerging class of hydrogels described by their mobile crosslinks, which are formed by rings topologically constrained to slide along linear polymer chains within the network. These materials have enjoyed decades of study by polymer chemists but have been underexplored by the tribology community. In this work, we synthesized a pseudo-rotaxane crosslinker from poly(ethylene glycol) diacrylate (PEG-diacrylate) and α-cyclodextrin-acrylate followed by hydrogel networks by connecting the sliding crosslinks with polyacrylamide chains. The mechanical and tribological properties of slide-ring hydrogels were investigated using a custom-built microtribometer. Slide-ring hydrogels exhibit unique behavior compared to conventional covalently crosslinked polyacrylamide hydrogels and offer a vast design space for future investigations.Graphical

Effects of Peierls phases in open linear chains

Effects of Peierls phases in open linear chains

Growth Patterns of Carbon Clusters Cn (n = 2-60) Identified via ABCluster Searching and DFT Benchmarking.

Recently, novel algorithms and enhanced computational capabilities have created unprecedented opportunities to precisely determine the geometric structures of clusters through theoretical calculations. In this study, we extensively investigated and characterized the geometric arrangements of the carbon clusters Cn (n = 2-60), employing the efficient ABCluster algorithm in conjunction with the gradient-corrected PBE and higher-accuracy B3LYP hybrid functional in density functional theory (DFT). New structures and a discernible structural growth pattern have been discovered. We observed a distinct preference in carbon clusters that transform from the linear chains (n = 2-9) to closed single-ring and planar structures (n = 10-27) and finally evolve to carbon cages (n = 28-60). A shortcut to construct the cage clusters was unveiled by inserting or rotating specific atoms within a distinct structural unit. The research results obtained from combining ABCluster with DFT calculations offer valuable new insights into the growth mechanisms and evolutionary trajectories of carbon clusters, providing a crucial theoretical framework for the development of innovative carbon-based materials and their potential applications.

Contributions of heterogeneous catalysis enabling resource efficiency and circular economy

Our industry today is predominantly based on linear value chains. Raw materials are extracted from primary sources, processed into products, used, and disposed of at the end of their life cycle. This linear economy causes a wide range of negative environmental impacts owing to the resulting greenhouse gas emissions and pollution of marine and terrestrial ecosystems. Closed carbon cycles and climate-neutral energy production are essential for the production not only of fuels but also of all chemicals, including plastics and fertilizers, to counteract climate change and further damage to the environment. In this regard, this article discusses the importance of heterogeneous catalysts for selected technologies associated with this transformation of the resource base and energy supply. It discusses the technological framework conditions of a net CO 2 -neutral industry, with a focus on electrocatalytic water-splitting for hydrogen production, as well as the catalytic challenges of production of chemicals for the whole value chain using biomass, CO 2 and plastic waste as raw materials. This article is part of the discussion meeting issue ‘Green carbon for the chemical industry of the future’.

Surface Plasmon Resonance Allows to Correlate Molecular Properties With Diffusion Coefficients of Linear Chain Alcohols.

Every biological and physicochemical process occurring in a fluid phase depends on the diffusion coefficient (D) of the species in solution. In the present work, a model to describe and fit the behaviour of as a function of structure and extensive thermodynamics parameters in binary solutions of linear chain organic molecules is developed. Supporting experimental and computational evidences for this model are obtained by measuring for a series of -alcohols through a novel surface plasmon resonance method and molecular dynamics simulations. This allows to propose a kind of combined analysis to explain the dependence of on various thermodynamic and structural parameters. The results suggest that for small linear systems in the range from 0 to 200 g mol-1 and under the assumption that the diffusive activation energy is a linear function of mass, is strictly dependent on the molecular shape and on the relative strength of the solute-solvent intermolecular forces represented by a parameter named R. The newly proposed approach can be utilized to characterize and monitor progressive changes in physicochemical properties for any investigated species upon increasing the dimension of the aggregate/molecule along a certain direction.

Diblock Rings as Topological Adhesives at Immiscible Polymer Interfaces.

Disparate polymers often do not mix well, and the resulting immiscible interfaces are mechanically weaker than the bulk, which is undesirable for many technological applications. Large-scale molecular simulations are performed to demonstrate the effectiveness of diblock ring polymers as a new type of adhesive for immiscible polymer interfaces. The peak stress σp and the failure strain γp upon shear deformation approach the bulk values with increasing diblock ring length and coverage. Breaking the diblock rings into pairs of diblock linear chains creates a reference system for comparison. The diblock rings increase both σp and γp compared to the diblock linear chains at the same coverage. Further topological analysis based on the Gauss Linking Number reveals that the threading of diblock rings by linear chains from the two opposite sides is the key mechanism for stronger adhesion, which is analogous to the hook-and-loop process in Velcro tape.

Bottlebrush Midblocks Promote Colloidal Bridging of Telechelic Polymers.

Telechelic polymers are effective rheological modifiers that bridge between associative constituents to form elastic networks. The performance of linear telechelic chains, however, is controlled by entropic forces and thus suffers from an upper limit on bridge formation. This work overcomes this limitation by utilizing telechelic triblock copolymers containing bottlebrush midblocks. By comparing the rheological properties of emulsions linked by telechelic bottlebrush polymers to those containing linear chains, we determined that telechelic polymers with bottlebrush midblocks form elastic networks more efficiently. These enhanced rheological properties arise from the high stiffness of the bottlebrush midblocks, which offsets the entropic stretching penalty for bridge formation, enabling them to more readily form networks. This molecular-level control over polymer conformation in complex fluids opens avenues for designing highly elastic networks with minimal polymeric additives.

Energy distributions of Frenkel–Kontorova-type atomic chains: Transition from conservative to dissipative dynamics

We investigate energy distributions of Frenkel–Kontorova-type atomic chains generated from large number of independent identically distributed (iid) random initial atomic positionings under two cases. In the first case, atoms at the free-end chains without dissipation (conservative case) are only coupled to one other atom, whereas each atom inside the bulk is coupled to its 2 nearest neighbors. Here, atoms located at the chain are all at the same type. Such kind of systems can be modelled by conservative standard map. We show that, when the coupling is non-linear (which leads chaotic arrangement of the atoms) for energy distribution, the Boltzmann–Gibbs statistical mechanics is constructed, namely, exponential form emerges as Boltzmann factor P(E)∝e−βE. However, when the coupling is linear (which leads linear arrangement of the atoms) the Boltzmann–Gibbs statistical mechanics fails and the exponential distribution is replaced by a q-exponential form, which generalizes the Boltzmann factor as P(E)∝eq−βqE=[1−(1−q)βqE]1/(1−q). We also show for each type of atom localization with N number of atoms, β (or βq) values can be given as a function of 1/N. In the second case, although the couplings among the atoms are exactly the same as the previous case, atoms located at the chain are now considered as being at different types. We show that, for energy distribution of such linear chains, each of the distributions corresponding to different dissipation parameters (γ) are in the q-exponential form. Moreover, we numerically verify that βq values can be given as a linear function of 1/∑n=1N(1−γ)(n−2). On the other hand, although energy distributions of the chaotic chains for different dissipation parameters are in exponential form, a linear scaling between β and γ values cannot be obtained. This scaling is possible if the energies of the chains are scaled with 1/(1−γ)−N. For both cases, clear data collapses among distributions are evident.

Measuring Topological Constraint Relaxation in Ring-Linear Polymer Blends.

Polymers are an effective test bed for studying topological constraints in condensed matter due to a wide array of synthetically available chain topologies. When linear and ring polymers are blended together, emergent rheological properties are observed as the blend can be more viscous than either of the individual components. This emergent behavior arises since ring-linear blends can form long-lived topological constraints as the linear polymers thread the ring polymers. Here, we demonstrate how the Gauss linking integral can be used to efficiently evaluate the relaxation of topological constraints in ring-linear polymer blends. For majority-linear blends, the relaxation rate of topological constraints depends primarily on reptation of the linear polymers, resulting in the diffusive time τ_{d,R} for rings of length N_{R} blended with linear chains of length N_{l} to scale as τ_{d,R}∼N_{R}^{2}N_{L}^{3.4}.

The Shigella flexneri effector IpaH1.4 facilitates RNF213 degradation and protects cytosolic bacteria against interferon-induced ubiquitylation.

A central signal that marshals host defense against many infections is the lymphocyte-derived cytokine interferon-gamma (IFNγ). The IFNγ receptor is expressed on most human cells and its activation leads to the expression of antimicrobial proteins that execute diverse cell-autonomous immune programs. One such immune program consists of the sequential detection, ubiquitylation, and destruction of intracellular pathogens. Recently, the IFNγ-inducible ubiquitin E3 ligase RNF213 was identified as a pivotal mediator of such a defense axis. RNF213 provides host protection against viral, bacterial, and protozoan pathogens. To establish infections, potentially susceptible intracellular pathogens must have evolved mechanisms that subdue RNF213-controlled cell-autonomous immunity. In support of this hypothesis, we demonstrate here that a causative agent of bacillary dysentery, Shigella flexneri, uses the type III secretion system (T3SS) effector IpaH1.4 to induce the degradation of RNF213. S. flexneri mutants lacking IpaH1.4 expression are bound and ubiquitylated by RNF213 in the cytosol of IFNγ-primed host cells. Linear (M1-) and lysine-linked ubiquitin is conjugated to bacteria by RNF213 independent of the linear ubiquitin chain assembly complex (LUBAC). We find that ubiquitylation of S. flexneri is insufficient to kill intracellular bacteria, suggesting that S. flexneri employs additional virulence factors to escape from host defenses that operate downstream from RNF213-driven ubiquitylation. In brief, this study identified the bacterial IpaH1.4 protein as a direct inhibitor of mammalian RNF213 and highlights evasion of RNF213-driven immunity as a characteristic of the human-tropic pathogen Shigella.

Unveiling the solution structure of a DNA duplex with continuous silver-modified Watson-Crick base pairs

The challenge of transforming organized DNA structures into their metallized counterparts persists in the scientific field. In this context, utilizing DNA molecules modified with 7-deazapurine, provides a transformative solution. In this study, we present the solution structure of a DNA duplex that can be transformed into its metallized equivalent while retaining the natural base pairing arrangement through the creation of silver-modified Watson-Crick base pairs. Unlike previously documented X-ray structures, our research demonstrates the feasibility of preserving the intrinsic DNA self-assembly while incorporating AgI into the double helix, illustrating that the binding of silver does not disrupt the canonical base-pairing organization. Moreover, in our case, the uninterrupted AgI chain deviates from forming conventional straight linear chains; instead, it adheres to a helical arrangement dictated by the underlying DNA structure. This research challenges conventional assumptions and opens the door to precisely design structures based on the organization of highly stable Ag-DNA assemblies.

Introducing Ion Mobility Mass Spectrometry in Brain Glycosaminoglycomics: Application to Chondroitin/Dermatan Sulfate Octasaccharide Domains.

Glycosaminoglycans (GAGs) are sulfated linear O-glycan chains abundantly expressed in the extracellular matrix (ECM). Among GAGs, chondroitin sulfate (CS) and dermatan sulfate (DS) play important roles at the brain level, where the distribution and location of the sulfates within the CS/DS chains are responsible for numerous biological events. The diversity of the neural hybrid CS/DS expressed in the brain and the need to elucidate their structure gave rise to considerable efforts toward the development of analytical methods able to discover novel regularly and irregularly sulfated domains. In this context, we report here the introduction of ion mobility separation (IMS) mass spectrometry (MS) in brain glycosaminoglycomics. Based on IMS MS and tandem MS (MS/MS) by collision-induced dissociation (CID), we have developed a powerful approach for the screening and structural analysis of neural CS/DS and optimized and validated the method for the structural analysis of octasaccharides that were released from brain proteoglycans by β-elimination and pooled after chain depolymerization using chondroitin AC lyase. The IMS MS data revealed the separation of CS/DS octamers into mobility families based on the amount of sulfation. Among the discovered oversulfated domains, of major biological importance is the pentasulfated-[4,5-Δ-GlcAGalNAc(IdoAGalNAc)3], for which the (-) nanoESI IMS CID MS/MS analysis disclosed through the presence of distinct drift times, the incidence of two isomers. Moreover, the generated fragment ions revealed an uncommon trisulfated motif and an uncommon pentasulfated motif. Hence, using IMS MS and CID MS/MS, novel brain-related CS/DS domains of atypical sulfation patterns were discovered and structurally characterized in detail.

Catalytic Appel Reaction Accessing the Mesoporous Substructure of a Robust and Heterogeneous Polyphosphamide

AbstractPolyphosphamides are normally good flame retardants. Herein a mesoporous polyphosphamide (p‐PPA) with an accessible average pore diameter of <10 nm and a surface area of 1.773 m2/g has been synthesized via condensation of 1,3‐diamino benzene (DAB) and phenyl phosphinic dichloride (PPDC). 31P, 13C CP‐MAS solid‐state NMR, Raman, and X‐ray photoelectron spectroscopic (XPS) characterizations confirm the presence of ‐{PV(O)‐NH}‐ in the repeating unit of the p‐PPA that is further used as a catalytic mediator to perform the Appel reaction i. e., conversion of alcohols to halides with a broad substrate scope and high TON (561). The heterogeneity of p‐PPA allows easy recovery of organic halides and recycling of the catalyst many times. Mesoporous p‐PPA has further given a scope to perform shape‐selective conversion of primary alcohols with linear alkyl chain (1‐dodecanol) while a low conversion for the bulky secondary (cyclo‐hexanol) and tertiary alcohol (tert‐butanol) is observed. Perhaps, the phosphamide units present inside the porous channel are non‐preferable sites for bulkier alcohols, as evident from the competitive experiments. A comparatively less catalytic conversion obtained with an analogous non‐porous n‐PPA, made of tris(2‐aminoethyl)amine (TREN) linker, highlights the role of porosity in p‐PPA to enhance the accessibility of numerous ‐{PV(O)‐NH}‐ reactive units to increase the TON.

Non‐Oxidative Dehydroaromatization of Linear Alkanes on Intermetallic Nanoparticles

There has been significant interest in developing new catalytic systems to convert linear chain alkanes into olefins and aromatics. In the case of higher alkanes (≥ C6), the production of aromatic compounds such as benzene‐toluene‐xylenes is highly desirable. However, as the length of the carbon chain increases, the dehydrogenation process becomes more complex, not only due to the challenges of C‐H activation but also the need for selectivity towards the desired products by the possibility of side reactions such as isomerization and cracking. Here, we present a detailed analysis of the dehydroaromatization of n‐hexane, n‐heptane, and n‐octane, using PtSn intermetallic nanoparticles supported on SBA‐15 as the catalyst. Through in‐situ spectroscopic and kinetic analysis, we have probed into the reaction kinetics, catalyst deactivation, and a mechanistic understanding of the dehydroaromatization process on the surface of the PtSn intermetallic nanoparticles. Introducing Sn has been shown to be crucial not only for enhancement of catalytic activity, but also for higher aromatics selectivity and stability on stream. Furthermore, the analysis of dehydroaromatization reaction rates of reactant and possible intermediates indicates that the dehydroaromatization of n‐hexane to benzene likely proceeds through initial dehydrogenation steps followed by ring closing.