Chemical Potential Research Articles

Phytochemical investigation and spectral characterization of isolated compounds from Pyracantha crenulata (D. Don) M. Roem (syn. Crataegus crenulata Roxb) leaves: evaluation of antioxidant activity and molecular docking analysis

Pyracantha crenulata (D. Don) M. Roem (syn. Crataegus crenulata Roxb.) is an evergreen shrub in the Rosaceae family, notable for its chemical diversity and biological potential. This study isolates and characterises six compounds (Cc-1 to Cc-6), including four new ones, using repeated column chromatography. Structural elucidation employed IR, UV-vis, 1H and 13 C NMR, and mass spectrometry. The DPPH assay was used to test the antioxidant activity in vitro. Compounds Cc-4, Cc-2, Cc-1, and Cc-5 had IC50 values of 15.734 μg/ml, 51.422 μg/ml, 62.864 μg/ml, and 71.622 μg/ml, in that order. Quantitative phytochemical analysis revealed flavonoid content (22.81 mg/g), tannin content (385.15 mg/g), and total phenolic content (128.78 mg/g). Human cyclin-dependent kinase 2 (CDK2) (PDB ID: 1hck) docked with compound Cc-4, which demonstrated strong antioxidant activity and revealed significant non-bonding interactions. The pkCSM and SwissADME analyses suggested promising drug-like properties for Cc-4, supported by BOILED-Egg diagrams highlighting its therapeutic potential.

CSEL-BGC: A Bioinformatics Framework Integrating Machine Learning for Defining the Biosynthetic Evolutionary Landscape of Uncharacterized Antibacterial Natural Products.

The sluggish pace of new antibacterial drug development reflects a vulnerability in the face of the current severe threat posed by bacterial resistance. Microbial natural products (NPs), as a reservoir of immense chemical potential, have emerged as the most promising avenue for the discovery of next generation antibacterial agent. Directly accessing the antibacterial activity of potential products derived from biosynthetic gene clusters (BGCs) would significantly expedite the process. To tackle this issue, we propose a CSEL-BGC framework that integrates machine learning (ML) techniques. This framework involves the development of a novel cascade-stacking ensemble learning (CSEL) model and the establishment of a groundbreaking model evaluation system. Based on this framework, we predict 6,666 BGCs with antibacterial activity from 3,468 complete bacterial genomes and elucidate a biosynthetic evolutionary landscape to reveal their antibacterial potential. This provides crucial insights for interpretating the synthesis and secretion mechanisms of unknown NPs.

Equations of State, Thermodynamics, and Miscibility Curves for Jovian Planet and Giant Exoplanet Evolutionary Models

The equation of state of hydrogen–helium (H–He) mixtures plays a vital role in the evolution and structure of gas giant planets and exoplanets. Recent equations of state that account for H–He interactions, coupled with H–He immiscibility curves, can now produce more physical evolutionary models, such as accounting for helium rain with greater fidelity than in the past. In this work, we present a set of tools for planetary evolution that provides a Python interface for existing tables of useful thermodynamic quantities, state-of-the-art H–He equations of state, and pressure-dependent H–He immiscibility curves. In particular, for a collection of independent variable choices, we provide scripts to calculate the variety of thermodynamic derivatives used to model convection and energy transport. These include the chemical potential derived from the internal energy, which is a modeling necessity in the presence of composition gradients when entropy is the other primary variable. Finally, an entropy-based convection formalism is presented and fully described that highlights the physical differences between adiabatic and isentropic interior models. This centralized resource is meant to facilitate both giant planet structural and evolutionary modeling and the entry of new research groups into the field of giant planet modeling. All tables of thermodynamic quantities and derivatives are available at https://github.com/Rob685/hhe_eos_misc, along with a unified Python interface. Tutorials demonstrating the interface are also available in the repository.

Comparative First-Principles Study of the Y2Ti2O7/Matrix Interface in ODS Alloys

Oxide-dispersion-strengthened (ODS) alloys generally exhibit extraordinary service performance under severe conditions through the formation of ultrafine nano oxides. Y2Ti2O7 has been characterized as the major strengthening oxide in Fe-based ODS alloys. First-principles energetic analyses were performed to investigate the structural, elastic and interface properties of Y2Ti2O7 in either Fe-based or Ni-based ODS alloys. Y2Ti2O7 has comparable elastic constants to bcc-Fe and fcc-Ni and similar elastic deformation compatibility in Y2Ti2O7-strengthened Fe-based and Ni-based ODS alloys is therefore expected. The Ni/oxide interface has generally better thermostability than Fe/oxide across the whole range of the concerned oxygen chemical potential. Further interface bonding and adhesion calculations revealed that Y2Ti2O7 can enhance the bonding strength of Ni/Y2Ti2O7 through d-d orbital interaction between the interfacial YTi layer and Ni layer, while the interface bonding between the Fe layer and YTi layer is weakened compared to the metal matrix. First-principles calculations suggest that Y2Ti2O7 can be a candidate for strengthening nano-oxides in either Fe-based or Ni-based ODS alloys with well-behaved mechanical properties for fourth-generation fission reactors and further experimental validations are encouraged.

Integration of MUTZ-Langerhans cells into a 3D full-thickness skin equivalent and influences of serum reduction and undefined medium supplements on differentiation

The MUTZ-3 cell line is a surrogate for Langerhans cells (LCs) employed in New Approach Methodologies for assessing the skin sensitizing potential of chemicals. However, MUTZ-3 cells must first be differentiated to achieve the LC-typical phenotype. As all protocols use high fetal calf serum (FCS) concentrations, we aimed at reducing, or even replacing FCS, while maintaining MUTZ-LC characteristics. Additionally, we assessed the impact of the poorly defined 5637-conditioned medium (5637CM) on MUTZ-LC differentiation.With reducing the FCS content by 75 %, the desired differentiation status was achieved after 7 instead of 14 days, identified by elevated CD207 and CD1a expression. Culture with Ultroser G, a synthetic surrogate for FCS, resulted in an insufficient number of MUTZ-LCs. 5 % FCS-differentiated MUTZ-LCs could be activated with DNCB, an extreme sensitizer, as demonstrated by increased CD83 expression. 5637CM did not affect MUTZ-LC differentiation and is therefore not needed as a supplement.For their intended role in an immunocompetent skin model to assess the sensitizing potential of chemicals, MUTZ-LCs were successfully integrated into the Phenion® Full-Thickness skin model, as demonstrated by CD1a expression. These results are important steps towards medium standardization and the generation of an immunocompetent skin model according to the 3R principles.

The role of water mobility on water-responsive actuation of silk

Biological water-responsive materials that deform with changes in relative humidity have recently demonstrated record-high actuation energy densities, showing promise as high-performance actuators for various engineering applications. However, there is a lack of theories capable of explaining or predicting the stress generated during water-responsiveness. Here, we show that the nanoscale confinement of water dominates the macroscopic dehydration-induced stress of the regenerated silk fibroin. We modified silk fibroin’s secondary structure, which leads to various distributions of bulk-like mobile and tightly bound water populations. Interestingly, despite these structure variations, all silk samples start to exert force when the bound-to-mobile (B/M) ratio of confined water reaches the same level. This critical B/M water ratio suggests a common threshold above which the chemical potential of water instigates the actuation. Our findings serve as guidelines for predicting and engineering silk’s WR behavior and suggest the potential of describing the WR behavior of biopolymers through confined water.

Statistical Thermodynamic Description of Self-Assembly of Large Inclusions in Biological Membranes.

Recent studies revealed anomalous underscreening in concentrated electrolytes, and we suggest that the underscreened electrostatic forces between membrane proteins play a significant role in the process of self-assembly. In this work, we assumed that the underscreened electrostatic forces compete with the thermodynamic Casimir forces induced by concentration fluctuations in the lipid bilayer, and developed a simplified model for a binary mixture of oppositely charged membrane proteins with different preference to liquid-ordered and liquid-disordered domains in the membrane. In the model, like macromolecules interact with short-range Casimir attraction and long-range electrostatic repulsion, and the cross-interaction is of the opposite sign. We determine energetically favored patterns in a system in equilibrium with a bulk reservoir of the macromolecules. Different patterns consisting of clusters and stripes of the two components and of vacancies are energetically favorable for different values of the chemical potentials. Effects of thermal flutuations at low temperature are studied using Monte Carlo simulations in grand canonical and canonical ensembles. For fixed numbers of the macromolecules, a single two-component cluster with a regular pattern coexists with dispersed small one-component clusters, and the number of small clusters depends on the ratio of the numbers of the molecules of the two components. Our results show that the pattern formation is controlled by the shape of the interactions, the density of the proteins, and the proportion of the components.

Translocation of Gaussian polymers across a nanometric cylindrical channel

We present an analytical model to study translocation of Gaussian polymers across a cylindrical channel of nanometric size with a chemical potential inside the channel. Results show that polymer conformational entropy generates an entropic M-like free energy barrier for translocation. The presence of a small negative chemical potential reduces the entropic free energy barrier rendering the translocation time to follow a power law τ = AN ν as function of polymer size N. Power law exponents ν found here in varying the channel radius R, run from 1.525 to 1.999 for unforced translocation, and from 1.594 to 2.006 for translocation with small chemical potentials when R = 1 nm. Presence of large negative chemical potentials generate a free energy well rendering the translocation time to follow an exponential growth τ = Ae α N . We show existence of a negative chemical potential μ c that minimizes the translocation time due to an interplay of conformational entropy and channel-polymer interactions. The translocation time as function of channel length L grows exponentially as τ = Ae cL , it runs from milliseconds up to decades in the range of lengths found in biological channels. Interestingly, small negative chemical potentials approaching μ c overcome the effect of large channel lengths reducing the translocation time below seconds. Translocation speeds <v(N) > show a maximum of micrometers per second then it decays with polymer size and channel length, the characteristic decay <v(N) > ∼ N −1 has been observed in previous experiments of voltage-driven DNA translocation.

Transitions between equilibrium and nonequilibrium phenomena in the description of crystal growth

The close intertwining of equilibrium and nonequilibrium thermodynamic representations and transitions between the two limiting principles of thermodynamics: the second beginning and the principle of least coercion (minimum entropy production in the stationary regime) constitute the main content of phenomenological theories of crystal growth. The difference of basic postulates of two sections of thermodynamics forces to discuss problems of reversibility and irreversibility of time, scales of observed phenomena and rules of conjugation of thermodynamic forces and flows in theories of crystal growth. A variant of the solution of some conjugation problems is shown on the example of the fluctuation model of dislocation crystal growth, which is based on the stationary isothermal process of thermodynamic free energy fluctuations. In the case of the limiting mode of adsorption of impurities on the crystal face according to the Langmuir model, the free energy fluctuations possessing the absence of the memory effect allow us to identify three chemical potentials of building particles that determine the corresponding values of solution supersaturations realized at different scale levels at the growing crystal face containing a helical dislocation. The supersaturations control quasi-equilibrium and nonequilibrium thermodynamic processes that constitute a single dislocation mechanism of crystal growth.

Theoretical Studies of the Electronic and Thermoelectric Properties of PrIn3 and NdIn3 in Cubic Phase

The electronic and thermoelectric properties of AB3 (A =Pr, Nd and B=In) materials (crystallizing in the cubic structure) having space group Pm-3m (221) are studied using B3PW91 hybrid functional through the Full-Potential Linear Augmented Plane Wave (FP-LAPW) approach within the framework of Density Functional Theory (DFT). The calculated lattice parameters for PrIn3 and NdIn3 are 4.5668 Å and 4.5539 Å respectively. Electron-electron correlation effect is due to the 4f orbitals present in these materials and therefore, with the use of B3PW91 hybrid functional, band structure and density of states are calculated. When analyzing electron charge density, these materials showed a stronger ionic character. Band structure and density of state analysis confirms the metallic nature of the materials. Using the semi-empirical Boltzmann approach implemented in the BoltzTraP code, the thermoelectric parameters, such as Seebeck coefficient, figure of merit, electrical conductivity per relaxation time, and electronic thermal conductivity per relaxation time as a function of chemical potential, were computed at 500 K temperature gradient. PrIn3 showed highest Seebeck coefficient value, 50.68 μV/K among these compounds. The peak value of electrical conductivity per relaxation time and electronic thermal conductivity per relaxation time among these compounds is calculated for NdIn3 is 2.43 x 1020 1/Ωms and 22.50×1014 W/mKs.

Testing the equivalence between the planar Gross-Neveu and Thirring models at N=1

It is known that the Fierz identities predict that the Gross-Neveu and Thirring models should be equivalent when describing systems composed of a single fermionic flavor, N=1. Here, we consider the planar version of both models within the framework of the optimized perturbation theory at the two-loop level, in order to verify if the predicted equivalence emerges explicitly when different temperature and density regimes are considered. At vanishing densities, our results indicate that both models indeed describe exactly the same thermodynamics, provided that N=1. However, at finite chemical potentials we find that the N=1 Fierz equivalence no longer holds. After examining the relevant thermodynamic potentials, we have identified the contributions which lead to this puzzling discrepancy. Finally, we discuss different frameworks in which this (so far open) problem could be further understood and eventually circumvented. Published by the American Physical Society 2024

Simulations evidencing two surface tensions for fluids confined in nanopores

As first recognized by Hill in 1960′s, one character distinguishing the thermodynamics of small systems from the macroscopic one is that some intensive variables are no longer defined uniquely for small systems. For example, the differential chemical potential, defined as the derivative of a thermodynamic potential with respect to particle number, is no longer equal to the integral one, given by the ratio of Gibbs free energy to the particle number. The concept of differential and integral surface tensions has been introduced recently to account for the increasing surface contribution to thermodynamic potentials when a system shrinks down in size. Simulations constitute a powerful tool for testing new concepts. The present work provides the simulation evidence for distinct differential and integral surface tensions. Our results point out some useful directions for future experimental investigations to check the general validity of the concept of differential and integral surface tensions.

A variational framework for Cahn–Hilliard-type diffusion coupled with Allen–Cahn-type multi-phase transformations in elastic and dissipative solids

This article presents a variational framework for coupled chemo-mechanical solids undergoing irreversible micro-structural changes at infinitesimal strains. The coupled problem is characterised by phenomena such as phase transitions, micro-structure coarsening and swelling. It is an extension of our previous work on variational inelasticity for a conserved chemo-mechanical setting to a unified conserved and non-conserved setting which include multi-phase transformations. The variational framework, again governed by continuous-time, discrete-time and discrete-space–time incremental variational principles, is outlined for coupled diffusion-phase transformation phenomena in elastic and dissipative solids. For the sake of simplicity, focus is restricted to isothermal conditions. It is shown that the governing macro- and micro-balance equations of the coupled problem appear as Euler equations of these minimisation and saddle point principles. In contrast to our previous work, extended variational principles (with the gradient of the chemical potential and phase fractions) are constructed that account for diffusion-phase transformation coupling. This is achieved by Legendre transformations. Note that the local–global solution strategy is still preserved and the resulting system of symmetric non-linear algebraic equations are solved by Newton–Raphson-type iterative methods. The applicability of the proposed framework is demonstrated by numerical simulations that qualitatively characterise lower bainitic micro-structure.

Pioneering bioinformatics with agent-based modelling: an innovative protocol to accurately forecast skin or respiratory allergic reactions to chemical sensitizers.

The assessment of theallergenic potential of chemicals, crucial for ensuring public health safety, faces challenges in accuracy and raises ethical concerns due to reliance on animal testing. This paper presents a novel bioinformatic protocol designed to address the critical challenge of predicting immune responses to chemical sensitizers without the use of animal testing. The core innovation lies in the integration of advanced bioinformatics tools, including the Universal Immune System Simulator (UISS), which models detailed immune system dynamics. By leveraging data from structural predictions and docking simulations, our approach provides a more accurate and ethical method for chemical safety evaluations, especially in distinguishing between skin and respiratory sensitizers. Our approach integrates a comprehensive eight-step process, beginning with the meticulous collection of chemical and protein data from databases like PubChem and the Protein Data Bank. Following data acquisition, structural predictions are performed using cutting-edge tools such as AlphaFold to model proteins whose structures have not been previously elucidated. This structural information is then utilized in subsequent docking simulations, leveraging both ligand-protein and protein-protein interactions to predict how chemical compounds may trigger immune responses. The core novelty of our method lies in the application of UISS-an advanced agent-based modelling system that simulates detailed immune system dynamics. By inputting the results from earlier stages, including docking scores and potential epitope identifications, UISS meticulously forecasts the type and severity of immune responses, distinguishing between Th1-mediated skin and Th2-mediated respiratory allergic reactions. This ability to predict distinct immune pathways is a crucial advance over current methods, which often cannot differentiate between the sensitization mechanisms. To validate the accuracy and robustness of our approach, we applied the protocol to well-known sensitizers: 2,4-dinitrochlorobenzene for skin allergies and trimellitic anhydride for respiratory allergies. The results clearly demonstrate the protocol's ability to differentiate between these distinct immune responses, underscoring its potential for replacing traditional animal-based testing methods. The results not only support the potential of our method to replace animal testing in chemical safety assessments but also highlight its role in enhancing the understanding of chemical-induced immune reactions. Through this innovative integration of computational biology and immunological modelling, our protocol offers a transformative approach to toxicological evaluations, increasing the reliability of safety assessments.

Improving thermoelectric performance of α−T3 structure via integration of the Kane-Mele-Hubbard model

Our research examines the electronic thermal conductivity, electrical conductivity, Seebeck coefficient, and figure of merit of the α-T3 structure utilizing the Green's function approach within the Hamiltonian framework of the Kane-Mele (KM) and Hubbard models. We evaluate how variations in chemical potential, on-site Coulomb repulsion (OSCR) strength, and spin-orbit coupling (SOC) parameters influence these properties. Our findings uncover interesting trends: the presence of a flat band at the energy level of zero within this structure and the gap between the flat band and other bands is observed. The observable rise in SOC results in a clear division within the energy band, demonstrating the notable impact SOC exerts on the electronic structure of the system.Moreover, this strategy displays that this material's thermoelectric properties increase due to temperature, SOC, and OSCR. Also, it was observed that augmenting the α parameter can enhance both thermoelectric and thermopower.

Aqueous extract of CAP-ash: A greener benchmark for Suzuki-Miyaura coupling reaction in palladium catalyzed ligand-free condition

Synthesis, molecular, spectroscopic properties, and electronic structure calculations of biphenyls derivatives have been achieved using a highly efficient catalytic amount of Pd(OAc)2 in aqueous extract of custard apple peels (CAP)-ash (AECAP) a green, highly cost-effective, operationally convenient and environmentally benign media at ambient temperature. The analytical reports showed the presence of metal oxides which are probably extracted in water produces corresponding hydroxides, which provide alkaline media in water which shows dual performance (solvent and base) for said cross-coupling transformation. The catalytic system is generated in situ based on aqueous extract and Pd(OAc)2 which requires no external base and ligand. Moreover, the study also offers insights into the frontier molecular orbitals (FMO), electronegativity, chemical potential, global electrophilicity index, ionization potential, electron affinity, chemical hardness, and softness properties of the synthesized biphenyl derivatives for understanding their stability, active sites, and biological activity using density functional theory (DFT) at the B3LYP/6–311G(d,p) level/basis.

Qualitative Profiling, Antioxidant and Antimicrobial Activities of Polar and Nonpolar Basil Extracts.

Basil (Ocimum basilicum L.) is a widely used culinary herb. In this study, ethanol, dichloromethane, and sunflower oil were used separately as solvents with distinct polarities for the extraction of basil aerial parts to simulate the different polarity conditions in domestic food processing. The oil extract (OE) was re-extracted with acetonitrile, and the chemical composition, antioxidant potential, and antimicrobial activities of the ethanol (EE), dichloromethane (DCME), and acetonitrile (ACNE) extracts were determined. A total of 109 compounds were tentatively identified in EE, DCME, and ACNE by HPLC-DAD/ESI-ToF-MS. Fatty acids were present in all extracts. Phenolic acids and flavonoids dominated in EE. DCME was characterised by triterpenoid acids, while diterpenoids were mainly found in ACNE. The extracts were analysed for their antioxidant capacity using the 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) assay. EE and DCME showed significant radical scavenging potential. Antimicrobial activity was explored in eight bacterial, two yeast, and one fungal species. All extracts exhibited high antifungal activity, comparable to or better than that of the commercial drug nistatin. Antibacterial activities were notable for EE and ACNE, while DCME showed no activity against bacteria in the applied concentration ranges. The different polarities of the solvents led to distinctive phytochemical compositions and bioactivities in the extracts.

Effect of particle size, water saturation, inorganic salt and methane on the phase equilibrium of CO2 hydrates in sediments

Understanding the thermal stability of gas hydrate in complex marine geological environment is of importance to hydrate-based carbon sequestration. In this work, the factors affecting the equilibrium of CO2 hydrate in ocean sediments, including quartz sands, inorganic salts and gas impurities were quantitatively measured in a temperature range from 273 to 283 K and a phase equilibrium model of hydrate was established. To reveal the distribution in pore structure, the micro-morphologies of hydrate-bearing sediments were measured by cryo-SEM. Results showed that reduction of initial water saturation, addition of NaCl and CH4 were found to have inhibitory effect on CO2 hydrate equilibrium. Initial water saturation reduced the equilibrium temperature by the capillary pressure, but only 0.3–0.7 K temperature depression was observed as the water saturation reduced to 5 %. About 5.7 K in the average temperature depression was found by the addition of 10 wt% NaCl and 24 mol% CH4. NaCl and CH4 influenced the hydrate equilibrium by changing the water activity and chemical potential of hydrate water lattice. SEM images showed that the hydrate formed in pores of quartz sand had porous surface and coated the sand particles like a layer of cells which are 5–20 μm in diameter, suggesting the hydrate layer exists between the liquid and gas phase. Based on the van der Waals-Platteeuw model, a hydrate equilibrium model was developed. The model provided a good prediction of the hydrate equilibrium in the presence of quartz sand, NaCl and CH4 with an averaged deviation of ±4.2 %, which had the potential to be applicated in more complexed ocean sedimentary environment.

Plasma-Plasma Third Order Phase Transition from Type IIB Supergravity.

We show that the planar, charged black hole in asymptotically anti-de Sitter spacetime, dual to the strongly coupled quark-gluon plasma thermal state of large N, SU(N), N=4 super Yang-Mills at finite chemical potential undergoes a third-order phase transition in the grand canonical ensemble to a hairy black hole of type IIB supergravity. The hairy phase is another strongly coupled fluid with a conformal equation of state and can be interpreted as another kind of quark-gluon plasma. This new quark-gluon plasma has less entropy and, therefore, seems to characterize some form of smooth hadronization. The locus of the transition in terms of the critical values of the "baryon" chemical potential μ_{c} and the temperature T_{c} is μ_{c}=2πT_{c}.

Combined extension and torsion of hydrogels with chemo-mechanical coupling: Revealing positive poynting effect

In this paper, combined extension and torsion of hydrogel subject to a chemo-mechanical coupled loading is described in the framework of continuum mechanics, where the free energy density consists of the elastic, mixing and chemical contributions. A simplified, closed-form and exactly analytical solution to the mechanical response is obtained, which accounts for the coupling effect of external loading, chemical potential and microstructural parameters, such as crosslinking degree, Flory-Huggins parameter, etc. In particular, the effect of free swelling and microscopic diffusion on deformation of the hydrogel at equilibrium state is discussed, reaching some fundamental conclusions. Negative axial forces are captured, revealing the typical positive Poynting effect where the cylinder tends to elongate on twisting, and an inhomogeneous deformation, induced by torsion, along the radial direction is demonstrated. Furthermore, the dynamic competition between external loading and solvent environment is revealed and investigated, where the direct connection between internal micro-physical parameters and macroscopic deformation is demonstrated. The theoretical results presented in this paper may provide predictions and guidance for the mechanical analysis and design of hydrogel cylinder subject to extension and torsion in a solvent.