Linear Chain Research Articles

Memory effects in disease modelling through kernel estimates with oscillatory time history

We design a linear chain trick algorithm for dynamical systems for which we have oscillatory time histories in the distributed time delay. We make use of this algorithmic framework to analyse memory effects in disease evolution in a population. The modelling is based on a susceptible-infected-recovered SIR—model and on a susceptible-exposed-infected-recovered SEIR—model through a kernel that dampens the activity based on the recent history of infectious individuals. This corresponds to adaptive behavior in the population or through governmental non-pharmaceutical interventions. We use the linear chain trick to show that such a model may be written in a Markovian way, and we analyze the stability of the system. We find that the adaptive behavior gives rise to either a stable equilibrium point or a stable limit cycle for a close to constant number of susceptibles, i.e. locally in time. We also show that the attack rate for this model is lower than it would be without the dampening, although the adaptive behavior disappears as time goes to infinity and the number of infected goes to zero.

Digital Transformation of Incumbent Pipeline Firms through Platformization

ABSTRACT Advancements in digital technology necessitate a shift from traditional linear buyer-supplier value chains to a network-centric approach facilitated by digital platforms. Despite digital platforms being a dominant model for transformation, limited research has explored the enablers for incumbent pipeline firms to embrace platformization. To address this gap, this study reviews existing literature on digital transformation, identifying nine enablers for digital platformization: changing client behavior, information technology (IT) capabilities development, structural efficiencies, disruptive competitive forces, scope advantages, economic triggers, disruptive third-party technology, creation of autonomous corporate structures, and regulatory compliance. Case studies of platformization in diverse industries are analyzed using the modified total interpretive structural modeling (m-TISM) approach, resulting in a hierarchical model with five levels. This model delineates interrelationships among trigger events, external enablers, internal organizational enablers, process enablers, and outcome drivers. Furthermore, the study highlights that the creation and extraction of value from digital platforms are operationalized through e-business strategies, contributing insights to e-business literature by discussing the implications of these enablers on dimensions such as commerce, collaboration, communication, connection, and computing.

The Jones polynomial in systems with periodic boundary conditions

Entanglement of collections of filaments arises in many contexts, such as in polymer melts, textiles and crystals. Such systems are modeled using periodic boundary conditions (PBCs), which create an infinite periodic system whose global entanglement may be impossible to capture and is repetitive. We introduce two new methods to assess topological entanglement in PBC: the Periodic Jones polynomial and the Cell Jones polynomial. These tools capture the grain of geometric/topological entanglement in a periodic system of open or closed chains, by using a finite link as a representative of the global system. These polynomials are topological invariants in some cases, but in general are sensitive to both the topology and the geometry of physical systems. For a general system of 1 closed chain in 1 PBC, we prove that the Periodic Jones polynomial is a recurring factor, up to a remainder, of the Jones polynomial of a conveniently chosen finite cutoff of arbitrary size of the infinite periodic system. We apply the Cell Jones polynomial and the Periodic Jones polynomial to physical PBC systems such as 3D realizations of textile motifs and polymer melts of linear chains obtained from molecular dynamics simulations. Our results demonstrate that the Cell Jones polynomial and the Periodic Jones polynomial can measure collective geometric/topological entanglement complexityin such systems of physical relevance.

SEB: a computational tool for symbolic derivation of the small-angle scattering from complex composite structures.

Analysis of small-angle scattering (SAS) data requires intensive modeling to infer and characterize the structures present in a sample. This iterative improvement of models is a time-consuming process. Presented here is Scattering Equation Builder (SEB), a C++ library that derives exact analytic expressions for the form factors of complex composite structures. The user writes a small program that specifies how the sub-units should be linked to form a composite structure and calls SEB to obtain an expression for the form factor. SEB supports e.g. Gaussian polymer chains and loops, thin rods and circles, solid spheres, spherical shells and cylinders, and many different options for how these can be linked together. The formalism behind SEB is presented and simple case studies are given, such as block copolymers with different types of linkage, as well as more complex examples, such as a random walk model of 100 linked sub-units, dendrimers, polymers and rods attached to the surfaces of geometric objects, and finally the scattering from a linear chain of five stars, where each star is built up of four diblock copolymers. These examples illustrate how SEB can be used to develop complex models and hence reduce the cost of analyzing SAS data.

Influence of solvent quality on the swelling and shear modulus of polymer gels chemically cross-linked in solution

The effect of temperature (T) is studied on the swelling of model poly(vinyl acetate) (PVAc) gels in isopropyl alcohol. The theta temperature Θ of these gels, at which the second osmotic virial coefficient A2 vanishes, is close to that of the corresponding high molecular mass polymer solution without cross-links so that solvent quality may be defined in the same way as the corresponding precursor polymer solution. We quantified the swelling and deswelling of PVAc gels relative to their size at the theta temperature, and also determined the effect of T on the shear modulus of these gels. It was found that both swelling and deswelling data could be reduced to a universal scaling equation of the same general form as derived from renormalization group (RG) theory for flexible linear polymer chains in solutions.Graphical abstractVariaton of the volumetric swelling factor as a function of the reduced temperature for PVAc gels swollen in isopropyl alcohol.

The Enhanced Thermoelectric and Mechanical Performance of Polythiophene/Single-Walled Carbon Nanotube Composites with Polar Ethylene Glycol Branched-Chain Modifications.

In order to develop flexible thermoelectric materials with thermoelectric and mechanical properties, in this study, we designed and synthesized polythiophene derivatives with branched ethylene glycol polar side-chains named P3MBTEMT, which were used in combination with single-walled carbon nanotubes (SWCNTs) to prepare composite thin films and flexible thermoelectric devices. A comparison was made with a polymer named P3(TEG)T, which has a polar alkoxy linear chain. The UV-vis results indicated that the larger steric hindrances of the branched ethylene glycol side-chain in P3MBTEMT could inhibit its self-aggregation and had a stronger interaction with the SWCNTs compared to that of P3(TEG)T, which was also confirmed using Raman spectroscopy. When the mass ratio of SWCNTs to P3MBTEMT was 9:1 (represented as P3MBTEMT/SWCNTs-0.9), the composite film exhibited the highest thermoelectric properties with a power factor of 446.98 μW m-1 K-2, which was more than two times higher than that of P3(TEG)T/SWCNTs-0.9 (215.08 μW m-1 K-2). The output power of the thermoelectric device with P3MBTEMT/SWCNTs-0.9 was 2483.92 nW at 50 K, which was 1.66 times higher than that of P3(TEG)T/SWCNTs-0.9 (1492.65 nW). Furthermore, the P3MBTEMT/SWCNTs-0.5 showed superior mechanical properties compared to P3(TEG)T/SWCNTs-0.5. These results indicated that the mechanical and thermoelectric performances of polymer/SWCNT composites could be significantly improved by adding polar branched side-chains to conjugated polymers. This study provided a new strategy for creating high-performing novel flexible thermoelectric materials.

Characterizing the Janus colloidal particles in AC electric field and a step towards label-free cargo manipulation

In recent years, researchers have been exploring Janus particles, a unique type of colloidal system, which has gained enormous attention across diverse fields, from soft matter physics to biology. These particles, possessing an asymmetric surface, can be manipulated in the fluid using external energy sources. This versatility makes them suitable for mimicking biological systems and applications like cargo transportation, drug delivery, biosensing, and environmental cleanup. The study focuses on the response of metal-dielectric (Ti-PMMA) Janus spheres in the AC field, created through the Physical Vapor Deposition (PVD) technique. When subjected to a uniform AC electric field, these particles exhibit different dynamic behaviors at various frequency ranges. The particles show diverse responses from induced-charge electrophoresis (ICEP: 500 Hz-80 kHz) to reversed motion (r: ICEP:100 kHz-1 MHz) and linear chain formation (1 MHz). Additionally, they randomly cluster near the lower characteristic frequency (800 Hz) of the ICEP, whereas they exhibit the 3D motion at frequencies (100 Hz) below this lower characteristic value. The mechanisms behind these dynamic phenomena could be explained by considering the concept of electric double layer (EDL), self-dielectrophoresis (sDEP), dipolar interactions, hydrodynamic interactions, and electrothermal effects. These active Janus Colloids are further leveraged to manipulate 1 µm diameter PMMA passive microparticles and E. coli bacteria at 1 kHz, showcasing their potential applications in cargo delivery under various microfluidic research areas. The manipulation of payloads could be explained based on dielectrophoretic trapping due to locally generated field gradients around the surface of the Janus sphere. Therefore, the present work offers an unprecedented opportunity to study such out-of-equilibrium complex active matter systems and create novel functional materials. Moreover, it could also be extended as a fuel-free microrobotics system for various biomedical applications such as sensing and on-demand drug or cargo delivery inside the microfluidics chamber.

Universal properties of branched copolymers in dilute solutions

We analyze the universal conformational properties of complex copolymer macromolecules, based on two topologies: the rosette structure containing fc linear branches and fr closed loops grafted to the central core, and the symmetric pom-pom structure, consisting of a backbone linear chain terminated by two branching points with functionalities f. We assume that the constituent strands (branches) of these structures can be of two different chemical species a and b. Depending on the solvent conditions, the inter- or intrachain interactions of some links may vanish, which corresponds to Θ-state of the corresponding polymer species. Applying both the analytical approach within the frames of direct polymer renormalization and numerical simulations based on the lattice model of polymer, we evaluated the set of parameters characterizing the size properties of constituent parts of two complex topologies and estimated quantitatively the impact of interactions between constituent parts on these size characteristics.

Multiscale Computational Framework for the Liquid-Liquid Phase Separation of Intrinsically Disordered Proteins.

The reversible assembly of intrinsically disordered proteins (IDPs) to form membraneless organelles (MLOs) is a fundamental process involved in the spatiotemporal regulation in living cells. MLOs formed via liquid-liquid phase separation (LLPS) serve as molecule-enhancing hubs to regulate cell functions. Owing to the complexity and dynamic nature of the protein assembly via a network of weak inter- and intra-molecular interactions, it is challenging to describe and predict the LLPS behavior. We have developed a multiscale computational model for IDPs, using the fused in sarcoma (FUS) protein and its variants as illustrative examples. To simplify the description of protein, FUS is represented as a linear chain of stickers interspaced by spacers, as inspired by the associative polymer theory. Low-complexity aromatic-rich kinked segments (LARKS) available in FUS were identified using LARKSdb and represented as "stickers". The pairwise potential energies of each pair of stickers and their β-sheet-forming propensity were estimated via molecular docking and all atomistic molecular dynamics (AA-MD) simulations. Subsequently, FUS chains were randomly positioned in a cubic lattice as coarse-grained (CG) beads, with the bead assignment based on the Kuhn length estimation of stickers and spacers. Stochastic FUS movements were modeled by Monte Carlo (MC) simulations. In addition to the Metropolis algorithm, discretized pair potential distributions between stickers were considered in the move acceptance criteria. The chosen pair potential represents one of the possible binding energy states, with its probability determined by the frequency of the binding energy distribution histogram. The fluctuations of averaged radial distribution functions (RDFs) in successive MC trial move intervals of equilibrated lattice MC simulations were used to indicate the dynamic nature of assembly/disassembly of the protein chains. This multiscale computational framework provides an economical and efficient way of predicting and describing the LLPS behavior of IDPs.

Supramolecular architecture of sodium heterocyclic dithiocarbamate salt: Insights from spectral analysis and bond valence sum characterization

The hydrated sodium salt of 1,2,3,4-tetrahydroquinolinedithiocarbamate (1) has been successfully synthesized and characterized using IR, NMR, and X-ray single crystal analysis. The υC–S and thioureide υC–N bands appeared at 1484 cm−1 and 968 cm−1, respectively, in Na(H2O)3+(thqdtc)– • H2O. The notable NCS2 carbon signal emerged at 212 ppm, credited to unique nitrogen and sulfur-induced deshielding effects. Compound 1 crystallizes in the monoclinic system, P21/c space group, with dimensions a = 14.4297(4) Å, b = 6.1534(2) Å, c = 17.6701(4) Å, β = 108.7340(10)°, V = 1485.83(7) Å3, and Z = 4. The structure of 1 exhibits a supramolecular architecture through secondary interactions, such as weak intermolecular interactions that link the molecules into a linear polymeric chain. The incorporation of heterocyclic rings in the dithiocarbamate ligands leads to the formation of an intriguing supramolecular architecture, as confirmed by BVS analysis results. The BVS value of sodium does not agree well with the formal oxidation state due to the interactions of anions, cations, coordinated and uncoordinated water molecules.

Reciprocity relations in a biologically inspired nanomagnonic system with dipolar coupling

Magnetosome chains in magnetotactic bacteria present ideal nanomagnonic model systems for studying collective resonance modes of dipolar-coupled single domain particles in relation to their spatial arrangement. Using microresonator-based ferromagnetic resonance (FMR) spectroscopy, electron microscopy, and micromagnetic modeling, we here provide insights into the complex magnonic activity within a single magnetosome chain. While the angular dependence of its FMR spectrum is dominated by twofold symmetry features due to the uniaxial anisotropy of linear chain segments, we also observed an unexpected behavior such as interrupted lines and flat bands due to the intricate geometrical details of this particular chain, such as a cross-like structural anomaly where a pair of particles is oriented perpendicular to the main axis of the chain and thus breaks the prevailing axial dipolar coupling symmetry. Such a cross junction formed by four particles exhibits interesting magnonic network properties. Notably, we observe reciprocity in the sense that the spectral response of one particle to an excitation of another one is identical to the response of the latter given an excitation of the former. Furthermore, we have identified that magnonic coupling between A and B can be facilitated via a dark state, as in magnonic stimulated Raman adiabatic passage, and that this dark-state coupling can be made non-reciprocal between A and B by breaking the symmetry of the spatial arrangement of the four particles.

Isolation of two peptaibols with potent antimicrobial and cytotoxic activities from the mangrove endophytic fungus Trichoderma lentiforme ML-P8-2

Trichorzin PA is a family of 18-residue peptaibols with linear and flexible peptide chains. The three-dimensional structures and biological activities of trichorzin PA peptaibols are largely uncharacterised. In this work, two previously identified peptaibols, trichorzin PA VI (1) and II (2), were isolated from Trichoderma lentiforme ML-P8-2. While for the first time, we report here the X-ray crystallographic structure of 1, antimicrobial activities against a panel of common pathogenic bacteria and fungi, and cytotoxicities of 1 and 2. In bioassays, 1 and 2 exhibited strong antimicrobial activities against the seven tested microbes, with MIC values in the range of 0.19–6.25 μM. Additionally, 1 and 2 displayed potent cytotoxicities against five human cancer cell lines, with IC50 values in the range of 0.01 ± 0.02–2.75 ± 0.17 μM. The bioassay results were generally better than those reported for other 18-residue peptaibols, including other trichorzin PA members.

Thermodynamic property estimations for aqueous primary, secondary, and tertiary alkylamines, benzylamines, and their corresponding aminiums across temperature and pressure are validated by measurements from experiments

On Earth and beyond, organic chemistry often occurs in the presence of water within environments that deviate drastically from ambient conditions (25 °C and 1 bar). Accurately predicting aqueous organic reaction pathways is crucial toward understanding planetary scale processes such as the cycling of elements crucial for life (e.g., carbon and nitrogen). Advanced thermodynamic modeling can be utilized to determine the favorability of various organic reactions based on geologically relevant ranges of temperature and pressure, as well as compositional variables (e.g., pH). However, data that would otherwise allow for a diversity of organic compounds and environmental conditions to be modeled are sparse and rarely tested with experiments, particularly with regard to organic-nitrogen compounds. In this work, we develop a framework to estimate thermodynamic properties at ambient conditions that can then be extrapolated across ranges of temperature and pressure for aqueous primary, secondary, and tertiary amines and aminiums (protonated amines), specifically those structures containing linear alkyl chains and benzyl functional groups. We also performed hydrothermal experiments (250 °C, ∼40 bar) involving reactions of methylamines to test our resulting thermodynamic models, and we compare our models for other alkylamines and benzylamines to previous empirical measurements from the literature. Specifically, we use existing thermodynamic data along with our estimates at ambient conditions in combination with a variety of existing extrapolation methods related to the revised Helgeson-Kirkham-Flowers (HKF) equations of state to generate temperature- and pressure-dependent predictions of acid dissociation constants (i.e., pKa values) that strongly agree with previous empirical measurements. We use similar methods to predict product distributions for reactions involving primary, secondary, and tertiary amines/aminiums, as well as ammonia/ammonium and corresponding alcohols whose collective distributions depend on reversible substitution reactions. Our predictions are in good agreement with our experimental results involving the methylamine reaction system as well as previous experiments involving the benzylamine reaction system, for which we also produced thermodynamic estimates involving benzyl alcohol. The agreement between independent theoretical predictions and experimental measurements suggests that our estimated properties can be applied to modeling amine chemistry in other experimental and natural aqueous systems that range in temperature and pressure, providing new tools for planetary exploration.

Two-step modification of pullulanase and transglucosidase: A novel way to improve the gel strength and reduce the digestibility of rice starch

The multiscale structure, gel strength and digestibility of rice starch modified by the two-step modification of pullulanase (PUL) pretreatment and transglucosidase (TG) treatment for 6, 12, 18 and 24 h were investigated. The debranching hydrolysis of PUL produced some linear chains, which rearranged to form stable crystalline structures, reducing the digestible starch content, but weakening the gel strength. TG treatment connected some short chains to longer linear chains via α-1,6-glycosidic bonds, generating the structures of linear chain with fewer branches. The short branches promoted the interaction between starch molecules to form a more compact three-dimensional gel network structure, showing higher hardness and springiness. Moreover, these chains could form more stable crystals, reducing the digestible starch content, and the increase of branching degree inhibited digestive enzyme hydrolysis, reducing the digestion rate. The multiscale structure of starch tended to stabilize after TG treatment for 18 h, which could form a gel with stronger strength and lower digestibility than native starch gel. Therefore, the two-step modification of PUL and TG was an effective way to change the structure of rice starch to improve the gel strength and reduce the digestibility.

Experimental realization of entangled coherent states in two-dimensional harmonic oscillators of a trapped ion

Entangled coherent states play pivotal roles in various fields such as quantum computation, quantum communication, and quantum sensing. We experimentally demonstrate the generation of entangled coherent states with the two-dimensional motion of a trapped ion system. Using Raman transitions with appropriate detunings, we simultaneously drive the red and blue sidebands of the two transverse axes of a single trapped ion and observe multi-periodic entanglement and disentanglement of its spin and two-dimensional motion. Then, by measuring the spin state, we herald entangled coherent states of the transverse motions of the trapped ion and observe the corresponding modulation in the parity of the phonon distribution of one of the harmonic oscillators. Lastly, we trap two ions in a linear chain and realize Mølmer–Sørensen gate using two-dimensional motion.

Molecular rheology of nanoconfined oligomer melts

We use nonequilibrium atomistic molecular dynamics simulations of unentangled melts of linear and star oligomer chains (C25H52) to study the steady-state viscoelastic response under confinement within nanoscale hematite (α−Fe2O3) channels. We report (i) the negative (positive) first (second) normal stress difference and (ii) the presence of viscoelastic tension at low Wi. With the aim of uncovering the molecular mechanism of viscoelasticity, we link these effects to bond alignment such that absorbed chains near the surface can carry the elastic force exerted on the walls, which decays as the chains become more aligned in the flow direction. This alignment is observed to be independent of the film thickness but enhanced as the shear rate increases or the surface attraction weakens.

Biochemical Characterization of Rice Xylan Biosynthetic Enzymes in Determining Xylan Chain Elongation and Substitutions.

Grass xylan consists of a linear chain of β-1,4-linked xylosyl residues that often form domains substituted only with either arabinofuranose (Araf) or glucuronic acid (GlcA)/methylglucuronic acid (MeGlcA) residues, and it lacks the unique reducing end tetrasaccharide sequence found in dicot xylan. The mechanism of how grass xylan backbone elongation is initiated and how its distinctive substitution pattern is determined remains elusive. Here, we performed biochemical characterization of rice xylan biosynthetic enzymes, including xylan synthases, glucuronyltransferases and methyltransferases. Activity assays of rice xylan synthases demonstrated that they required short xylooligomers as acceptors for their activities. While rice xylan glucuronyltransferases effectively glucuronidated unsubstituted xylohexaose acceptors, they transferred little GlcA residues onto (Araf)-substituted xylohexaoses and rice xylan 3-O-arabinosyltransferase could not arabinosylate GlcA-substituted xylohexaoses, indicating that their intrinsic biochemical properties may contribute to the distinctive substitution patterns of rice xylan. In addition, we found that rice xylan methyltransferase exhibited a low substrate binding affinity, which may explain the partial GlcA methylation in rice xylan. Furthermore, immunolocalization of xylan in xylem cells of both rice and Arabidopsis showed that it was deposited together with cellulose in secondary walls without forming xylan-rich nanodomains. Together, our findings provide new insights into the biochemical mechanisms underlying xylan backbone elongation and substitutions in grass species.

A Game Theoretical Analysis of Non-linear Blockchain System

Recent advances in blockchain research have been made in two important directions. One is refined resilience analysis utilizing game theory to study the consequences of selfish behavior of users (miners), and the other is the extension from a linear (chain) structure to a non-linear (graphical) structure for performance improvements, such as IOTA and Graphcoin. The first question that comes to mind is what improvements a blockchain system would see by leveraging these new advances. In this article, we consider three major properties for a blockchain system: α-partial verification, scalability, and finality-duration. We establish a formal framework and prove that no blockchain system can achieve α-partial verification for any fixed constant α, high scalability, and low finality-duration simultaneously. We observe that classical blockchain systems like Bitcoin achieve full verification (α =1) and low finality-duration, Ethereum 2.0 Sharding achieves low finality-duration and high scalability. We are interested in whether it is possible to partially satisfy the three properties.

Molecular dynamics study of water molecules nucleation for fine particle removal: Effects of wettability and aggregation modes and comparison with experiment

Water vapor nucleation on particle's surface plays an important role in dust removal, cloud formation, and particle measurement. However, the selectivity of nucleation sites and the nucleation characteristic of water molecule on the particle's surface are still unclear, especially for the aggregated particles. In this paper, the effects of particle wettability and aggregation modes on the selectivity of nucleation sites and the nucleation characteristics were investigated using molecular dynamics simulation. The results were compared with our earlier experimental findings. It illustrates how the contact angle of clusters, the growth velocity, and the growth duration are all influenced by the interaction coefficient between water and particles. Moreover, the nucleation sites of water molecules on the particle aggregation surface exhibit a definite selectivity. The primary indicator of this selectivity is the preferential nucleation of water molecules at the interfaces of linear chain aggregation particles, at the inner side of non-linear chain aggregation particles, and at the centers of ring aggregation. These results are in good agreement with our previous experimental findings. More significantly, additional research has revealed that subcritical-size clusters typically aggregate on two-particle surfaces spacing when the spacing smaller than the critical cluster size.

Temperature dependence of the dynamics and interfacial width in nanoconfined polymers via atomistic simulations.

We present a detailed computational study on the temperature effect of the dynamics and the interfacial width of unentangled cis-1,4 polybutadiene linear chains confined between strongly attractive alumina layers via long, several μs, atomistic molecular dynamics simulations for a wide range of temperatures (143-473 K). We examine the spatial gradient of the translational segmental dynamics and of an effective local glass temperature (TgL). The latter is found to be much higher than the bulk Tg for the adsorbed layer. It gradually reduces to the bulk Tg at about 2nm away from the substrate. For distant regions (more than ≈1.2nm), a bulk-like behavior is observed; relaxation times follow a typical Vogel-Fulcher-Tammann dependence for temperatures higher than Tg and an Arrhenius dependence for temperatures below the bulk Tg. On the contrary, the polymer chains at the vicinity of the substrate follow piecewise Arrhenius processes. For temperatures below about the adsorbed layer's TgL, the translational dynamics follows a bulk-like (same activation energy) Arrhenius process. At higher temperatures, there is a low activation energy Arrhenius process, caused by high interfacial friction forces. Finally, we compute the interfacial width, based on both structural and dynamical definitions, as a function of temperature. The absolute value of the interfacial width depends on the actual definition, but, regardless, the qualitative behavior is consistent. The interfacial width peaks around the bulk Tg and contracts for lower and higher temperatures. At bulk Tg, the estimated length of the interfacial width, computed via the various definitions, ranges between 1.0 and 2.7nm.