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1
Bonilla, Steve L., Sarah K. Denny, John H. Shin, Aurora Alvarez-Buylla, William J. Greenleaf, and Daniel Herschlag. "High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs." Proceedings of the National Academy of Sciences 118, no. 33 (August 9, 2021): e2109085118. http://dx.doi.org/10.1073/pnas.2109085118.
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Despite RNA’s diverse secondary and tertiary structures and its complex conformational changes, nature utilizes a limited set of structural “motifs”—helices, junctions, and tertiary contact modules—to build diverse functional RNAs. Thus, in-depth descriptions of a relatively small universe of RNA motifs may lead to predictive models of RNA tertiary conformational landscapes. Motifs may have different properties depending on sequence and secondary structure, giving rise to subclasses that expand the universe of RNA building blocks. Yet we know very little about motif subclasses, given the challenges in mapping conformational properties in high throughput. Previously, we used “RNA on a massively parallel array” (RNA-MaP), a quantitative, high-throughput technique, to study thousands of helices and two-way junctions. Here, we adapt RNA-MaP to study the thermodynamic and conformational properties of tetraloop/tetraloop receptor (TL/TLR) tertiary contact motifs, analyzing 1,493 TLR sequences from different classes. Clustering analyses revealed variability in TL specificity, stability, and conformational behavior. Nevertheless, natural GAAA/11ntR TL/TLRs, while varying in tertiary stability by ∼2.5 kcal/mol, exhibited conserved TL specificity and conformational properties. Thus, RNAs may tune stability without altering the overall structure of these TL/TLRs. Furthermore, their stability correlated with natural frequency, suggesting thermodynamics as the dominant selection pressure. In contrast, other TL/TLRs displayed heterogenous conformational behavior and appear to not be under strong thermodynamic selection. Our results build toward a generalizable model of RNA-folding thermodynamics based on the properties of isolated motifs, and our characterized TL/TLR library can be used to engineer RNAs with predictable thermodynamic and conformational behavior.
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Soni, Surbhi, Gunjan Chauhan, Bhawna Pareek, Pankaj Sharma, and Rajan Chopra. "Binary Liquid Mixtures Nonanol and Decanol with their Thermodynamic and Transport Behavior: A Review." Research Journal of Chemistry and Environment 26, no. 9 (August 25, 2022): 167–74. http://dx.doi.org/10.25303/2609rjce1670174.
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The extensive knowledge about structural phenomena of mixtures is of indispensable importance in the development of theories in liquid state. The information about structural and molecular interactions of liquid mixtures is quite vital from both fundamental and engineering point of view and can be utilized for further studies. For a better understanding of the non-ideal behavior of complex systems, fundamental thermodynamic and thermo-physical properties are the varied sources in which information is required. The excess thermodynamic properties are very sensitive to variables such as size, shape, composition, temperature and pressure, therefore an important information about the differences in the intermolecular interactions was obtained using these binary liquid mixtures under a range of physiochemical conditions. By using thermodynamics quantities, we can calculate the deviation of thermodynamics properties from those of an ideal mixture. These properties are necessary for the development of thermodynamic models required in optimized processes of the chemical, petrochemical, pharmaceutical and other industries. Along with diverse industrial applications, binary liquid mixtures can have hazardous effects such as pollutants causing air, water and soil contamination and some of them may have cancerous features. Their organic compounds and derivatives prepared from them are employed in a range of industrial and consumer applications such as perfumes, cosmetics, paints, varnishes, drugs, fuels, explosives, fats, dyes, waxes, resins, plastics, rubber, detergents, DDT etc. making them commercially important.
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Gujrati, Purushottam Das. "Foundations of Nonequilibrium Statistical Mechanics in Extended State Space." Foundations 3, no. 3 (August 23, 2023): 419–548. http://dx.doi.org/10.3390/foundations3030030.
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The review provides a pedagogical but comprehensive introduction to the foundations of a recently proposed statistical mechanics (μNEQT) of a stable nonequilibrium thermodynamic body, which may be either isolated or interacting. It is an extension of the well-established equilibrium statistical mechanics by considering microstates mk in an extended state space in which macrostates (obtained by ensemble averaging A^) are uniquely specified so they share many properties of stable equilibrium macrostates. The extension requires an appropriate extended state space, three distinct infinitessimals dα=(d,de,di) operating on various quantities q during a process, and the concept of reduction. The mechanical process quantities (no stochasticity) like macrowork are given by A^dαq, but the stochastic quantities C^αq like macroheat emerge from the commutator C^α of dα and A^. Under the very common assumptions of quasi-additivity and quasi-independence, exchange microquantities deqk such as exchange microwork and microheat become nonfluctuating over mk as will be explained, a fact that does not seem to have been appreciated so far in diverse branches of modern statistical thermodynamics (fluctuation theorems, quantum thermodynamics, stochastic thermodynamics, etc.) that all use exchange quantities. In contrast, dqk and diqk are always fluctuating. There is no analog of the first law for a microstate as the latter is a purely mechanical construct. The second law emerges as a consequence of the stability of the system, and cannot be violated unless stability is abandoned. There is also an important thermodynamic identity diQ≡diW≥0 with important physical implications as it generalizes the well-known result of Count Rumford and the Gouy-Stodola theorem of classical thermodynamics. The μNEQT has far-reaching consequences with new results, and presents a new understanding of thermodynamics even of an isolated system at the microstate level, which has been an unsolved problem. We end the review by applying it to three different problems of fundamental interest.
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Mei, Baicheng, Yuxing Zhou, and Kenneth S. Schweizer. "Experimental test of a predicted dynamics–structure–thermodynamics connection in molecularly complex glass-forming liquids." Proceedings of the National Academy of Sciences 118, no. 18 (April 26, 2021): e2025341118. http://dx.doi.org/10.1073/pnas.2025341118.
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Understanding in a unified manner the generic and chemically specific aspects of activated dynamics in diverse glass-forming liquids over 14 or more decades in time is a grand challenge in condensed matter physics, physical chemistry, and materials science and engineering. Large families of conceptually distinct models have postulated a causal connection with qualitatively different “order parameters” including various measures of structure, free volume, thermodynamic properties, short or intermediate time dynamics, and mechanical properties. Construction of a predictive theory that covers both the noncooperative and cooperative activated relaxation regimes remains elusive. Here, we test using solely experimental data a recent microscopic dynamical theory prediction that although activated relaxation is a spatially coupled local–nonlocal event with barriers quantified by local pair structure, it can also be understood based on the dimensionless compressibility via an equilibrium statistical mechanics connection between thermodynamics and structure. This prediction is found to be consistent with observations on diverse fragile molecular liquids under isobaric and isochoric conditions and provides a different conceptual view of the global relaxation map. As a corollary, a theoretical basis is established for the structural relaxation time scale growing exponentially with inverse temperature to a high power, consistent with experiments in the deeply supercooled regime. A criterion for the irrelevance of collective elasticity effects is deduced and shown to be consistent with viscous flow in low-fragility inorganic network-forming melts. Finally, implications for relaxation in the equilibrated deep glass state are briefly considered.
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Nashed, Gamal. "General form of the analytic function f(T) in diverse dimension for a static planar spacetime." International Journal of Modern Physics D 28, no. 12 (September 2019): 1950158. http://dx.doi.org/10.1142/s021827181950158x.
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We derive an exact static solution in diverse dimension, without any constraints, to the field equations of [Formula: see text] gravitational theory using a planar spacetime with two unknown functions, i.e. [Formula: see text] and [Formula: see text]. The black hole solution is characterized by two constants, [Formula: see text] and [Formula: see text], one is related to the mass of the black hole, [Formula: see text], and the other is responsible to make the solution deviate from the teleparallel equivalent of general relativity (TEGR). We show that the analytic function [Formula: see text] depends on the constant [Formula: see text] and becomes constant function when [Formula: see text] which corresponds to the TEGR case. The interesting property of this solution is the fact that it makes the singularity of the Kretschmann invariant much softer than the TEGR case. We calculate the energy of this black hole and show that it is equivalent to ADM mass. Applying a coordinate transformation, we derive a rotating black hole with nontrivial values of the torsion scalar and [Formula: see text]. Finally, we examine the physical properties of this black hole solution using the laws of thermodynamics and show that it has thermodynamical stability.
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Guvench, Olgun, Devon Martin, and Megan Greene. "Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins." International Journal of Molecular Sciences 23, no. 1 (December 31, 2021): 473. http://dx.doi.org/10.3390/ijms23010473.
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The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between 4C1 and 1C4 chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids.
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Casanellas, Jordi, and Ilídio Lopes. "The Sun and stars: Giving light to dark matter." Modern Physics Letters A 29, no. 37 (December 4, 2014): 1440001. http://dx.doi.org/10.1142/s021773231440001x.
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During the last century, with the development of modern physics in such diverse fields as thermodynamics, statistical physics, and nuclear and particle physics, the basic principles of the evolution of stars have been successfully well understood. Nowadays, a precise diagnostic of the stellar interiors is possible with the new fields of helioseismology and astroseismology. Even the measurement of solar neutrino fluxes, once a problem in particle physics, is now a powerful probe of the core of the Sun. These tools have allowed the use of stars to test new physics, in particular the properties of the hypothetical particles that constitute the dark matter (DM) of the Universe. Here we present recent results obtained using this approach.
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Hassan, Mohsan, Sajid Ali, Walid Aich, Faical Khlissa, Badreddine Ayadi, and Lioua Kolsi. "Transport pattern of Non-Newtonian mass and thermal energy under two diverse flow conditions by using modified models for thermodynamics properties." Case Studies in Thermal Engineering 29 (January 2022): 101714. http://dx.doi.org/10.1016/j.csite.2021.101714.
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Hofmeister, Anne M. "Dependence of Heat Transport in Solids on Length-Scale, Pressure, and Temperature: Implications for Mechanisms and Thermodynamics." Materials 14, no. 2 (January 18, 2021): 449. http://dx.doi.org/10.3390/ma14020449.
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Accurate laser-flash measurements of thermal diffusivity (D) of diverse bulk solids at moderate temperature (T), with thickness L of ~0.03 to 10 mm, reveal that D(T) = D∞(T)[1 − exp(−bL)]. When L is several mm, D∞(T) = FT−G + HT, where F is constant, G is ~1 or 0, and H (for insulators) is ~0.001. The attenuation parameter b = 6.19D∞−0.477 at 298 K for electrical insulators, elements, and alloys. Dimensional analysis confirms that D → 0 as L → 0, which is consistent with heat diffusion, requiring a medium. Thermal conductivity (κ) behaves similarly, being proportional to D. Attenuation describing heat conduction signifies that light is the diffusing entity in solids. A radiative transfer model with 1 free parameter that represents a simplified absorption coefficient describes the complex form for κ(T) of solids, including its strong peak at cryogenic temperatures. Three parameters describe κ with a secondary peak and/or a high-T increase. The strong length dependence and experimental difficulties in diamond anvil studies have yielded problematic transport properties. Reliable low-pressure data on diverse thick samples reveal a new thermodynamic formula for specific heat (∂ln(cP)/∂P = −linear compressibility), which leads to ∂ln(κ)/∂P = linear compressibility + ∂lnα/∂P, where α is thermal expansivity. These formulae support that heat conduction in solids equals diffusion of light down the thermal gradient, since changing P alters the space occupied by matter, but not by light.
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Currie, Simon L., and Michael K. Rosen. "Using quantitative reconstitution to investigate multicomponent condensates." RNA 28, no. 1 (November 12, 2021): 27–35. http://dx.doi.org/10.1261/rna.079008.121.
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Many biomolecular condensates are thought to form via liquid–liquid phase separation (LLPS) of multivalent macromolecules. For those that form through this mechanism, our understanding has benefitted significantly from biochemical reconstitutions of key components and activities. Reconstitutions of RNA-based condensates to date have mostly been based on relatively simple collections of molecules. However, proteomics and sequencing data indicate that natural RNA-based condensates are enriched in hundreds to thousands of different components, and genetic data suggest multiple interactions can contribute to condensate formation to varying degrees. In this Perspective, we describe recent progress in understanding RNA-based condensates through different levels of biochemical reconstitutions as a means to bridge the gap between simple in vitro reconstitution and cellular analyses. Complex reconstitutions provide insight into the formation, regulation, and functions of multicomponent condensates. We focus on two RNA–protein condensate case studies: stress granules and RNA processing bodies (P bodies), and examine the evidence for cooperative interactions among multiple components promoting LLPS. An important concept emerging from these studies is that composition and stoichiometry regulate biochemical activities within condensates. Based on the lessons learned from stress granules and P bodies, we discuss forward-looking approaches to understand the thermodynamic relationships between condensate components, with the goal of developing predictive models of composition and material properties, and their effects on biochemical activities. We anticipate that quantitative reconstitutions will facilitate understanding of the complex thermodynamics and functions of diverse RNA–protein condensates.
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Rogers, Joseph M., Toby Passioura, and Hiroaki Suga. "Nonproteinogenic deep mutational scanning of linear and cyclic peptides." Proceedings of the National Academy of Sciences 115, no. 43 (October 9, 2018): 10959–64. http://dx.doi.org/10.1073/pnas.1809901115.
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High-resolution structure–activity analysis of polypeptides requires amino acid structures that are not present in the universal genetic code. Examination of peptide and protein interactions with this resolution has been limited by the need to individually synthesize and test peptides containing nonproteinogenic amino acids. We describe a method to scan entire peptide sequences with multiple nonproteinogenic amino acids and, in parallel, determine the thermodynamics of binding to a partner protein. By coupling genetic code reprogramming to deep mutational scanning, any number of amino acids can be exhaustively substituted into peptides, and single experiments can return all free energy changes of binding. We validate this approach by scanning two model protein-binding peptides with 21 diverse nonproteinogenic amino acids. Dense structure–activity maps were produced at the resolution of single aliphatic atom insertions and deletions. This permits rapid interrogation of interaction interfaces, as well as optimization of affinity, fine-tuning of physical properties, and systematic assessment of nonproteinogenic amino acids in binding and folding.
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Holubec, Viktor, Artem Ryabov, Sarah A. M. Loos, and Klaus Kroy. "Equilibrium stochastic delay processes." New Journal of Physics 24, no. 2 (February 1, 2022): 023021. http://dx.doi.org/10.1088/1367-2630/ac4b91.
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Abstract Stochastic processes with temporal delay play an important role in science and engineering whenever finite speeds of signal transmission and processing occur. However, an exact mathematical analysis of their dynamics and thermodynamics is available for linear models only. We introduce a class of stochastic delay processes with nonlinear time-local forces and linear time-delayed forces that obey fluctuation theorems and converge to a Boltzmann equilibrium at long times. From the point of view of control theory, such ‘equilibrium stochastic delay processes’ are stable and energetically passive, by construction. Computationally, they provide diverse exact constraints on general nonlinear stochastic delay problems and can, in various situations, serve as a starting point for their perturbative analysis. Physically, they admit an interpretation in terms of an underdamped Brownian particle that is either subjected to a time-local force in a non-Markovian thermal bath or to a delayed feedback force in a Markovian thermal bath. We illustrate these properties numerically for a setup familiar from feedback cooling and point out experimental implications.
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SINGH, Prabhat, and Dharmahinder Singh CHAND. "VIGV Angle Optimization for Subsonic Axial Flow Compressor." INCAS BULLETIN 12, no. 2 (June 5, 2020): 217–28. http://dx.doi.org/10.13111/2066-8201.2020.12.2.18.
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Long-term performance of an axial-flow compressor by the scheduling of inlet guide vanes at off-design conditions has been studied in this paper. The compressors are used in various industries and in aviation sectors for different operations at different climatic conditions; due to diverse climatic conditions the compressor is unable to give good performances as expected. At the design conditions, the results show that the variations in total pressure loss coefficient, volume flow rate, pressure ratio, and others like thermodynamics, aerodynamic properties are different at different stagger angles of 15°, 30° and 45°. BladeGen tools were used to design the inlet guide vanes for the investigations. The performance parameters of the axial flow compressor were analyzed by using ANSYS CFX and were validated using the analytical method. The objective of this study is to minimize the total pressure loss coefficient and improve the aerodynamic characteristics of an inlet guide vanes at different stagger angles and hence reduce the overall fuel consumption. The outcomes of this work give an improved insight into the efficient use of a VIGV in axial flow compressor.
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Sarazen, Michele L., and Enrique Iglesia. "Stability of bound species during alkene reactions on solid acids." Proceedings of the National Academy of Sciences 114, no. 20 (May 1, 2017): E3900—E3908. http://dx.doi.org/10.1073/pnas.1619557114.
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This study reports the thermodynamics of bound species derived from ethene, propene, n-butene, and isobutene on solid acids with diverse strength and confining voids. Density functional theory (DFT) and kinetic data indicate that covalently bound alkoxides form C–C bonds in the kinetically relevant step for dimerization turnovers on protons within TON (0.57 nm) and MOR (0.67 nm) zeolitic channels and on stronger acids HPW (polyoxometalate clusters on silica). Turnover rates for mixed alkenes give relative alkoxide stabilities; the respective adsorption constants are obtained from in situ infrared spectra. Tertiary alkoxides (from isobutene) within larger voids (MOR, HPW) are more stable than less substituted isomers but are destabilized within smaller concave environments (TON) because framework distortions are required to avoid steric repulsion. Adsorption constants are similar on MOR and HPW for each alkoxide, indicating that binding is insensitive to acid strength for covalently bound species. DFT-derived formation free energies for alkoxides with different framework attachments and backbone length/structure agree with measurements when dispersion forces, which mediate stabilization by confinement in host–guest systems, are considered. Theory reveals previously unrecognized framework distortions that balance the C–O bond lengths required for covalency with host–guest distances that maximize van der Waals contacts. These distortions, reported here as changes in O-atom locations and dihedral angles, become stronger for larger, more substituted alkoxides. The thermodynamic properties reported here for alkoxides and acid hosts differing in size and conjugate-anion stability are benchmarked against DFT-derived free energies; their details are essential to design host–guest pairs that direct alkoxide species toward specific products.
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Bai, Liuyang, Yuge Ouyang, Jun Song, Zhi Xu, Wenfu Liu, Jingyu Hu, Yinling Wang, and Fangli Yuan. "Synthesis of Metallic Nanocrystals: From Noble Metals to Base Metals." Materials 12, no. 9 (May 8, 2019): 1497. http://dx.doi.org/10.3390/ma12091497.
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Metallic nanocrystals exhibit superior properties to their bulk counterparts because of the reduced sizes, diverse morphologies, and controllable exposed crystal facets. Therefore, the fabrication of metal nanocrystals and the adjustment of their properties for different applications have attracted wide attention. One of the typical examples is the fabrication of nanocrystals encased with high-index facets, and research on their magnified catalytic activities and selections. Great accomplishment has been achieved within the field of noble metals such as Pd, Pt, Ag, and Au. However, it remains challenging in the fabrication of base metal nanocrystals such as Ni, Cu, and Co with various structures, shapes, and sizes. In this paper, the synthesis of metal nanocrystals is reviewed. An introduction is briefly given to the metal nanocrystals and the importance of synthesis, and then commonly used synthesis methods for metallic nanocrystals are summarized, followed by specific examples of metal nanocrystals including noble metals, alloys, and base metals. The synthesis of base metal nanocrystals is far from satisfactory compared to the tremendous success achieved in noble metals. Afterwards, we present a discussion on specific synthesis methods suitable for base metals, including seed-mediated growth, ligand control, oriented attachment, chemical etching, and Oswald ripening, based on the comprehensive consideration of thermodynamics, kinetics, and physical restrictions. At the end, conclusions are drawn through the prospect of the future development direction.
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KOLOBE, Doris, Yasien SAYED, and Heini W. DIRR. "Characterization of bromosulphophthalein binding to human glutathione S-transferase A1-1: thermodynamics and inhibition kinetics." Biochemical Journal 382, no. 2 (August 24, 2004): 703–9. http://dx.doi.org/10.1042/bj20040056.
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In addition to their catalytic functions, GSTs (glutathione S-transferases) bind a wide variety of structurally diverse non-substrate ligands. This ligandin function is known to result in the inhibition of catalytic function. The interaction between hGSTA1-1 (human class Alpha GST with two type 1 subunits) and a non-substrate anionic ligand, BSP (bromosulphophthalein), was studied by isothermal titration calorimetry and inhibition kinetics. The binding isotherm is biphasic, best described by a set of two independent sites: a high-affinity site and a low-affinity site(s). The binding stoichiometries for these sites are 1 and 3 molecules of BSP respectively. BSP binds to the high-affinity site 80 times more tightly (Kd=0.12 μM) than it does to the low-affinity site(s) (Kd=9.1 μM). Binding at these sites is enthalpically and entropically favourable, with no linkage to protonation events. Temperature- and salt-dependent studies indicate the significance of hydrophobic interactions in the binding of BSP, and that the low-affinity site(s) displays low specificity towards the anion. Binding of BSP results in the release of ordered water molecules at these hydrophobic sites, which more than offsets unfavourable entropic changes during binding. BSP inhibition studies show that the binding of BSP to its high-affinity site does not inhibit hGSTA1-1. This site, located near Trp-20, may be related to the buffer-binding site observed in GSTP1-1. The low-affinity-binding site(s) for BSP is most probably located at or near the active site of hGSTA1-1. Binding to this site(s) results in non-competitive inhibition with respect to CDNB (1-chloro-2,4-dinitrobenzene) (KiBSP=16.8±1.9 μM). Given the properties of the H site and the relatively small size of the electrophilic substrate CDNB, it is plausible that the active site of the enzyme can simultaneously accommodate both BSP and CDNB. This would explain the non-competitive behaviour of certain inhibitors that bind the active site (e.g. BSP).
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Destainville, Nicolas, Manoel Manghi, and Julie Cornet. "A Rationale for Mesoscopic Domain Formation in Biomembranes." Biomolecules 8, no. 4 (September 29, 2018): 104. http://dx.doi.org/10.3390/biom8040104.
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Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also be observed in vitro on model systems such as supported membranes or lipid vesicles. Lipid mixtures separating in liquid-ordered and liquid-disordered phases below a demixing temperature play a pivotal role in this context. Protein-protein and protein-lipid interactions also contribute to membrane shaping by promoting small domains or clusters. Such phase separations displaying characteristic length-scales falling in-between the nanoscopic, molecular scale on the one hand and the macroscopic scale on the other hand, are named mesophases in soft condensed matter physics. In this review, we propose a classification of the diverse mechanisms leading to mesophase separation in biomembranes. We distinguish between mechanisms relying upon equilibrium thermodynamics and those involving out-of-equilibrium mechanisms, notably active membrane recycling. In equilibrium, we especially focus on the many mechanisms that dwell on an up-down symmetry breaking between the upper and lower bilayer leaflets. Symmetry breaking is an ubiquitous mechanism in condensed matter physics at the heart of several important phenomena. In the present case, it can be either spontaneous (domain buckling) or explicit, i.e., due to an external cause (global or local vesicle bending properties). Whenever possible, theoretical predictions and simulation results are confronted to experiments on model systems or living cells, which enables us to identify the most realistic mechanisms from a biological perspective.
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Bychkova, Svetlana A. N., Galina G. N. Gorboletova, and Kseniya O. N. Frolova. "STUDY OF COMPLEX FORMATION OF Co (II) WITH TRIGLYCINE IN AQUEOUS SOLUTION." IZVESTIYA VYSSHIKH UCHEBNYKH ZAVEDENII KHIMIYA KHIMICHESKAYA TEKHNOLOGIYA 63, no. 2 (February 8, 2020): 21–25. http://dx.doi.org/10.6060/ivkkt.20206302.6020.
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Peptides are an extensive class of both natural and synthetic organic compounds, many of which have high and diverse physiological activity. The relevance of the study of the complexing properties of tripeptides is determined by the large value of these compounds in biological processes, since peptides are a simplified fragment of proteins and are widely used in various sectors of the pharmaceutical industry. One of the representatives of low molecular weight tripeptides is glycyl-glycyl-glycine. In this work, the complex formation of triglycine with Co2+ ions at 298.15 K and I = 0.2 mol/l (KNO3) was studied by potentiometric titration. The study of the complexing properties of triglycine with Co2+ was carried out by the method of potentiometric titration with the ratios M:L = 1:1, 1:2, 1:5. For processing the experimental data, the universal program PHMETR was used, designed to calculate equilibrium constants with an arbitrary number of reactions from the measured equilibrium concentration of one of the particles. The existence of CoL, CoH-1L, CoL2 CoH-2L22–, CoL3–, CoH-3L34– complexes was established. Their stability constants were determined. And the probable structures of the resulting complexes were proposed. The results of this study show that the oxygen and nitrogen atoms of the peptide group are involved in the processes of interaction between Co(II) and triglycine. This significantly changes the thermodynamics of the complex formation of short peptides in comparison with amino acids. The stability constants of cobalt (II) triglycinates obtained in this work allow one to carry out mathematical modeling of equilibria in multicomponent solutions, to predict the behavior of systems in a wide range of concentrations and pH. They can form the basis for generalizations concerning the structure and behavior of low molecular weight peptides in solution, and used for further studies, including calorimetric ones.
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Devoie, Élise G., Stephan Gruber, and Jeffrey M. McKenzie. "A repository of measured soil freezing characteristic curves: 1921 to 2021." Earth System Science Data 14, no. 7 (July 20, 2022): 3365–77. http://dx.doi.org/10.5194/essd-14-3365-2022.
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Abstract. Soil freeze–thaw processes play a fundamental role in the hydrology, geomorphology, ecology, thermodynamics, and soil chemistry of cold regions' landscapes. In understanding these processes, the temperature of the soil is used as a proxy to represent the partitioning of soil ice and water content via a soil freezing characteristic curve (SFCC). This mathematical construct relates the soil ice content to a specific temperature for a particular soil. SFCCs depend on many factors, including soil properties (e.g., porosity and composition), soil pore water pressure, dissolved salts, (hysteresis in) freezing/thawing point depression, and the degree of saturation, all of which can be site-specific and time-varying characteristics. SFCCs have been measured using various methods for diverse soils since 1921, but, to date, these data have not been broadly compared. This is in part because they had not previously been compiled in a single dataset. The dataset presented in this publication includes SFCC data digitized or received from authors, and it includes both historic and modern studies. The data are stored in an open-source repository, and an R package is available to facilitate their use. Aggregating the data has pointed out some data gaps, namely that there are few studies on coarse soils and comparably few in situ measurements of SFCCs in mountainous environments. It is hoped that this dataset (https://doi.org/10.5281/zenodo.5592825; Devoie et al., 2022a) will aid in the development of SFCC theory and improve SFCC approximations in soil freeze–thaw modelling activities.
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Dingcong, Roger G., Daryl B. Radjac, Fortia Louise Adeliene M. Alfeche, Arniel Ching O. Dizon, Kassandra Jayza Gift D. Tejas, Roberto M. Malaluan, Harith H. Al-Moameri, Gerard G. Dumancas, Arnold C. Alguno, and Arnold A. Lubguban. "An Iterative Method for the Simulation of Rice Straw-Based Polyol Hydroxyl Moieties." Sustainability 15, no. 15 (August 7, 2023): 12082. http://dx.doi.org/10.3390/su151512082.
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Bio-derived polyol products have gained global interest as a green and sustainable substitute for fossil-based polyols in a diverse range of polyurethane (PU) applications. According to previous studies, PU properties are highly influenced by the reaction kinetics during their formation. One major factor affecting this is the reactivity of their polyol’s functional hydroxyl moieties that are classified as primary, secondary, and hindered-secondary. However, experimental quantitative characterization of these polyol hydroxyl moieties remains a challenge in the field due to various factors affecting them, including extensive time requirements, the need for substantial and expensive resources, large potential errors, and the generation of wastes, as well as health and safety considerations. In this study, the molar fraction of primary, secondary, and hindered-secondary hydroxyl moieties of a petroleum-based polyol (V490) and a rice straw-based polyol were determined via an iterative computational method. The method employed a MATLAB script that can simultaneously solve multiple differential equations involving PU gelling reaction kinetics and thermodynamics. In this manner, numerical combinations of the fraction of each type of hydroxyl moiety are generated by looping together the respective numerical fractions for each moiety. The best-fit combinations of the fractions of the mixed polyol’s hydroxyl moieties were successfully found via curve fitting of the simulated and experimental gelling temperature profile with an average numerical deviation of less than 1%. Thus, the method presented in this study offers a faster and more reliable characterization of the polymeric reaction kinetics than the experimental and conventional computational methods for product property enhancement and development in the field.
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Fu, Zhi Jian, Li Jun Jia, and Wei Long Quan. "Phase Transition and ThermodynamicProperties of OsN2 under High Pressure." Applied Mechanics and Materials 401-403 (September 2013): 660–62. http://dx.doi.org/10.4028/www.scientific.net/amm.401-403.660.
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The lattice parameters, phase transition, and thermodynamic properties of OsN2in pyrite and fluorite structure are investigated by first-principles calculations. The pressure and temperature induced phase transitions of OsN2from fluorite structure to pyrite structure have been obtained. It is found that the transition pressure of OsN2at zero temperature is 158.2 GPa, and there exists no transition temperature. In addition, the thermal expansion, the Debye temperature, and the Grüneisen parameter in diverse pressures and temperatures about these two structures have also been obtained. Key words: transition phase; thermodynamic properties; OsN2PACS numbers: 71.15.Mb, 64.70.Kb
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Shephard, J. J., S. K. Callear, S. Imberti, J. S. O. Evans, and C. G. Salzmann. "Microstructures of negative and positive azeotropes." Physical Chemistry Chemical Physics 18, no. 28 (2016): 19227–35. http://dx.doi.org/10.1039/c6cp02450e.
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Azeotropes famously impose fundamental restrictions on distillation processes, yet their special thermodynamic properties make them highly desirable for a diverse range of industrial and technological applications. Using neutron diffraction, this study provides first insights into the microstructures of azeotropes.
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Deng, Gao-Ming, and Yong-Chang Huang. "Q − Φ criticality and microstructure of charged AdS black holes in f(R) gravity." International Journal of Modern Physics A 32, no. 35 (December 20, 2017): 1750204. http://dx.doi.org/10.1142/s0217751x17502049.
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The phase transition and critical behaviors of charged AdS black holes in [Formula: see text] gravity with a conformally invariant Maxwell (CIM) source and constant curvature are further investigated. As a highlight, this research is carried out by employing new state parameters [Formula: see text] and contributes to deeper understanding of the thermodynamics and phase structure of black holes. Our analyses manifest that the charged [Formula: see text]-CIM AdS black hole undergoes a first-order small–large black hole phase transition, and the critical behaviors qualitatively behave like a Van der Waals liquid–vapor system. However, differing from the case in Einstein’s gravity, phase structures of the black holes in [Formula: see text] theory exhibit an interesting dependence on gravity modification parameters. Moreover, we adopt the thermodynamic geometry to probe the black hole microscopic properties. The results show that, on the one hand, both the Ruppeiner curvature and heat capacity diverge exactly at the critical point, on the other hand, the [Formula: see text]-CIM AdS black hole possesses the property as ideal Fermi gases. Of special interest, we discover a microscopic similarity between the black holes and a Van der Waals liquid–vapor system.
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Maślanka, Anna, Jan Krzek, Mariusz Stolarczyk, Maria Walczak, and Agata Głogowska. "Stability Studies of Clonazepam, Diazepam, Haloperidol, and Doxepin with Diverse Polarities in an Acidic Environment." Journal of AOAC INTERNATIONAL 94, no. 6 (November 1, 2011): 1791–99. http://dx.doi.org/10.5740/jaoacint.10-083.
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Abstract Stability of clonazepam, diazepam, haloperidol, and doxepin was determined in acidic solutions. In addition, determination of the kinetic and thermodynamic properties of this stability was carried out. Reaction rate constants (k), half-life times (t0.1 and t0.5), and activation energy (Ea) were estimated for the drugs, which differed in polarity expressed with log P values. It was observed that estimated E a values increased from 42.13 to 125.03 kJ/mol with an increase of lipophilicity (log P) beginning from the most hydrophilic drug (clonazepam, 2.70 log P) to the most lipophilic drug (doxepin, 4.10 log P). All degradation products were studied using an HPLC/electrospray ionization-MS technique in the positive ionization mode.
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Okamoto, Isao, and Osamu Kaburaki. "The third law of thermodynamics for Kerr black holes." Monthly Notices of the Royal Astronomical Society 250, no. 2 (May 1991): 300–309. http://dx.doi.org/10.1093/mnras/250.2.300.
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Abstract At first the thermodynamic and evolutionary properties of Kerr black holes are clarified using the M–J plane, where M is the hole’s mass and J is its angular momentum. In this plane Schwarzschild black holes with h = 0 are distributed along the M-axis and extreme Kerr holes with h = 1 lie on the line J = M2, where $h \equiv J/4S$ is a non-dimensional parameter and S is the entropy. Taking into account possible accretion processes, we then derive the condition under which the third law of black-hole thermodynamics for Kerr holes is not violated. The condition is given in the form of as $\alpha \ge 1$, where the rate of change of a hole’s state, dh/dM, is proportional to $(1-h)^\alpha$ in the neighbourhood of $h \simeq 1$. If the rate is proportional to the vanishing surface gravity, gH, with which the hole has to accrete matter and angular momentum, α is given by $\alpha= 1+2/C$, where $dh/dM=Cg_\text H=C(1-h^2)/4M$, and C is a proportionality constant. In this case M, J and S diverge to infinity as a power law for $h \to 1$, and therefore no Kerr holes can reach the extreme Kerr state with the absolute zero temperature by accreting finite amounts of mass and angular momentum.
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Victor Ferreira da Silva, Paulo, and Orivaldo Da Silva Lacerda Júnior. "THERMODYNAMIC ASPECTS OF GASES IDEALITY." Journal of Interdisciplinary Debates 3, no. 02 (July 3, 2022): 86–116. http://dx.doi.org/10.51249/jid.v3i02.806.
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This work deals with a thermodynamic approach to the ideality of gases in a systematic and organized way. Important aspects are presented regarding the understanding of the behavior of gases and their properties, such as the properties of the physical state of matter, in which the gas is in the simplest state according to the arrangement of its molecules. It was highlighted the topics that led the scientists to arrive at the knowledge currently available, through experimental results observed by them, resulting in empirical laws that helped to understand the behavior of the gases in diverse situations, as in the cases of variations of temperature and pressure. These laws, which combined proportionately, resulted in a mathematical equation called the perfect or ideal gas equation, a law that strictly follows the formulated empirical mathematical relations and which is the starting point for the deduction of what is really the ideal or perfect gas. The gas model quoted is the basis of the kinetic theory of gases, which theory has a well-developed theoretical understanding to explain the behavior of an ideal gas. Also exposed in this work is the definition of real gases that present different behavior of the ideal gases due to the interactions that can occur between their molecules. For a better understanding of the real gases we explained ways of studying the intermolecular forces in these gases, such as the compressibility factor and the Van der Waals equation. Also, the transformations occurring in the gaseous state, such as liquefaction, are discussed. The present work was done on the basis of bibliographical research in order to have a favorable knowledge about the study of gases from the thermodynamic point of view, aiming to establish the necessary definitions of the study of the phases of matter.
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Cantwell, Patrick R., Timofey Frolov, Timothy J. Rupert, Amanda R. Krause, Christopher J. Marvel, Gregory S. Rohrer, Jeffrey M. Rickman, and Martin P. Harmer. "Grain Boundary Complexion Transitions." Annual Review of Materials Research 50, no. 1 (July 1, 2020): 465–92. http://dx.doi.org/10.1146/annurev-matsci-081619-114055.
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Grain boundaries can undergo phase-like transitions, called complexion transitions, in which their structure, composition, and properties change discontinuously as temperature, bulk composition, and other parameters are varied. Grain boundary complexion transitions can lead to rapid changes in the macroscopic properties of polycrystalline metals and ceramics and are responsible for a variety of materials phenomena as diverse as activated sintering and liquid-metal embrittlement. The property changes caused by grain boundary complexion transitions can be beneficial or detrimental. Grain boundary complexion engineering exploits beneficial complexion transitions to improve the processing, properties, and performance of materials. Here, we review the thermodynamic fundamentals of grain boundary complexion transitions, highlight the strongest experimental and computationalevidence for these transitions, clarify a number of important misconceptions, discuss the advantages of grain boundary complexion engineering, and summarize existing research challenges.
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Nedvěd, Daniel, Petr Hošek, Petr Klíma, and Klára Hoyerová. "Differential Subcellular Distribution of Cytokinins: How Does Membrane Transport Fit into the Big Picture?" International Journal of Molecular Sciences 22, no. 7 (March 26, 2021): 3428. http://dx.doi.org/10.3390/ijms22073428.
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Cytokinins are a class of phytohormones, signalling molecules specific to plants. They act as regulators of diverse physiological processes in complex signalling pathways. It is necessary for plants to continuously regulate cytokinin distribution among different organs, tissues, cells, and compartments. Such regulatory mechanisms include cytokinin biosynthesis, metabolic conversions and degradation, as well as cytokinin membrane transport. In our review, we aim to provide a thorough picture of the latter. We begin by summarizing cytokinin structures and physicochemical properties. Then, we revise the elementary thermodynamic and kinetic aspects of cytokinin membrane transport. Next, we review which membrane-bound carrier proteins and protein families recognize cytokinins as their substrates. Namely, we discuss the families of “equilibrative nucleoside transporters” and “purine permeases”, which translocate diverse purine-related compounds, and proteins AtPUP14, AtABCG14, AtAZG1, and AtAZG2, which are specific to cytokinins. We also address long-distance cytokinin transport. Putting all these pieces together, we finally discuss cytokinin distribution as a net result of these processes, diverse in their physicochemical nature but acting together to promote plant fitness.
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Ge, Ni-Na, Yong-Kai Wei, Jia-Jin Tan, Guang-Fu Ji, and Yan Cheng. "Physical properties of osmium dinitride with fluorite, pyrite, marcasite, and monoclinic structures under high pressure: First-principles study." Canadian Journal of Physics 93, no. 4 (April 2015): 424–33. http://dx.doi.org/10.1139/cjp-2014-0228.
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The structure, phase transition, elastic, and thermodynamic properties of OsN2 have been studied via first-principles calculations. It is shown that the CoSb2 structure is more stable than other structures. By the calculated H-P relations at 0 K, we found that the phase transition of OsN2 from CoSb2 structure to marcasite structure (ε → δ) occurs at 16.8 GPa, while the phase transition pressure between pyrite structure and fluorite structure (γ → α) is 80 GPa. The results of obtained phase transitions are also confirmed by bond length, sound velocity, and thermal expansion coefficient under different pressures. The pressure dependences of the elastic constants, mechanical stability, and mechanical anisotropy of four structures of OsN2 have been investigated by finding that the fluorite (pyrite and marcasite) structure OsN2 is mechanically stable under hydrostatic pressure (up to 60 GPa). However, the monoclinic structure is mechanically unstable under pressure from 0 to 60 Gpa. The calculated elastic anisotropic factors show that OsN2 possesses high elastic anisotropy under pressure. Moreover, the calculations on total density of states show that OsN2 of different structures has a metallic character, in agreement with previous theoretical results. The thermodynamic properties and sound velocity under diverse pressures of OsN2 of the four structures have been also investigated successfully.
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Romero, Carmen M., Andrea P. Escamilla, Ana C. F. Ribeiro, and Miguel A. Esteso. "Effect of 1,2-propanediol on the Critical Micelle Concentration of Decyltrimethylammonium Bromide at Temperatures from 293.15 K to 308.15 K." International Journal of Molecular Sciences 23, no. 24 (December 14, 2022): 15884. http://dx.doi.org/10.3390/ijms232415884.
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It is well known that polar organic compounds, such as alcohols and polyols, exert an appreciable influence on water structure and thus have important effects on surfactant micellization. These substances are often used to modify the properties of surfactants in aqueous solutions, increasing the practical applications they have in diverse industries. In this work, the critical micelle concentration (CMC) of decyltrimethylammonium bromide (C10TAB) in water and in 1,2-propanediol aqueous solutions was determined from both sound velocity and surface tension measurements as a function of surfactant concentration in the temperature range of (293.15 to 308.15) K. The critical micelle concentration of the surfactant increases as the concentration of 1,2-propanediol becomes higher, while the effect on temperature does not show important changes within the range considered. At the selected temperatures, the standard thermodynamic parameters of micellization suggests that the addition of 1,2-propanediol makes the micellization process less favorable. Thermodynamic analysis suggests that the micelle formation of C10TAB is an entropy-driven process at the temperatures considered in this study.
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Al-Fahdi, Mohammed, Alejandro Rodriguez, Tao Ouyang, and Ming Hu. "High-Throughput Computation of New Carbon Allotropes with Diverse Hybridization and Ultrahigh Hardness." Crystals 11, no. 7 (July 5, 2021): 783. http://dx.doi.org/10.3390/cryst11070783.
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The discovery of new carbon allotropes with different building blocks and crystal symmetries has long been of great interest to broad materials science fields. Herein, we report several hundred new carbon allotropes predicted by the state-of-the-art RG2 code and first-principles calculations. The types of new carbon allotropes that were identified in this work span pure sp2, hybrid sp2/sp3, and pure sp3 C–C bonding. All structures were globally optimized at the first-principles level. The thermodynamic stability of some selected carbon allotropes was further validated by computing their phonon dispersions. The predicted carbon allotropes possess a broad range of Vickers’ hardness. This wide range of Vickers’ hardness is explained in detail in terms of both atomic descriptors such as density, volume per atom, packing fraction, and local potential energy throughout the unit cell, and global descriptors such as elastic modulus, shear modulus, and bulk modulus, universal anisotropy, Pugh’s ratio, and Poisson’s ratio. For the first time, we found strong correlation between Vickers’ hardness and average local potentials in the unit cell. This work provides deep insight into the identification of novel carbon materials with high Vickers’ hardness for modern applications in which ultrahigh hardness is desired. Moreover, the local potential averaged over the entire unit cell of an atomic structure, an easy-to-evaluate atomic descriptor, could serve as a new atomic descriptor for efficient screening of the mechanical properties of unexplored structures in future high-throughput computing and artificial-intelligence-accelerated materials discovery methods.
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Hoffman, Alexander E. J., Jelle Wieme, Sven M. J. Rogge, Louis Vanduyfhuys, and Veronique Van Speybroeck. "The impact of lattice vibrations on the macroscopic breathing behavior of MIL-53(Al)." Zeitschrift für Kristallographie - Crystalline Materials 234, no. 7-8 (July 26, 2019): 529–45. http://dx.doi.org/10.1515/zkri-2018-2154.
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Abstract The mechanism inducing the breathing in flexible metal-organic frameworks, such as MIL-53(Al), is still not fully understood. Herein, the influence of lattice vibrations on the breathing transition in MIL-53(Al) is investigated to gain insight in this phenomenon. Through solid-state density-functional theory calculations, the volume-dependent IR spectrum is computed together with the volume-frequency relations of all vibrational modes. Furthermore, important thermodynamic properties such as the Helmholtz free energy, the specific heat capacity, the bulk modulus, and the volumetric thermal expansion coefficient are derived via these volume-frequency relations using the quasi-harmonic approximation. The simulations expose a general volume-dependency of the vibrations with wavenumbers above 300 cm−1 due to their localized nature. In contrast, a diverse set of volume-frequency relations are observed for vibrations in the terahertz region (<300 cm−1) containing the vibrations exhibiting collective behavior. Some terahertz vibrations display large frequency differences over the computed volume range, induced by either repulsion or strain effects, potentially triggering the phase transformation. Finally, the impact of the lattice vibrations on the thermodynamic properties is investigated. This reveals that the closed pore to large pore phase transformation in MIL-53(Al) is mainly facilitated by terahertz vibrations inducing rotations of the organic linker, while the large pore to closed pore phase transformation relies on two framework-specific soft modes.
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Wu, Ying, Zhou Li, Hui Feng, and Shuang He. "Atomic Interactions and Order–Disorder Transition in FCC-Type FeCoNiAl1-xTix High-Entropy Alloys." Materials 15, no. 11 (June 3, 2022): 3992. http://dx.doi.org/10.3390/ma15113992.
Full textAbstract:
Single-phase high-entropy alloys with compositionally disordered elemental arrangements have excellent strength, but show a serious embrittlement effect with increasing strength. Precipitation-hardened high-entropy alloys, such as those strengthened by L12-type ordered intermetallics, possess a superior synergy of strength and ductility. In this work, we employ first-principles calculations and thermodynamic simulations to explore the atomic interactions and order–disorder transitions in FeCoNiAl1−xTix high-entropy alloys. Our calculated results indicate that the atomic interactions depend on the atomic size of the alloy components. The thermodynamic stability behaviors of L12 binary intermetallics are quite diverse, while their atomic arrangements are short-range in FeCoNiAl1−xTix high-entropy alloys. Moreover, the order–disorder transition temperatures decrease with increasing Ti content in FeCoNiAl1−xTix high-entropy alloys, the characteristics of order–disorder transition from first-principles calculations are in line with experimental observations and CALPHAD simulations. The results of this work provide a technique strategy for proper control of the order–disorder transitions that can be used for further optimizing the microstructure characteristics as well as the mechanical properties of FeCoNiAl1−xTix high-entropy alloys.
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Peterková, Kateřina, Ivo Durník, Radek Marek, Janez Plavec, and Peter Podbevšek. "c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry." Nucleic Acids Research 49, no. 15 (August 7, 2021): 8947–60. http://dx.doi.org/10.1093/nar/gkab659.
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Abstract Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
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Obeso-Jureidini, Juan Carlos, Daniela Olascoaga, and Victor Romero-Rochín. "Thermodynamic Derivation of Scaling at the Liquid–Vapor Critical Point." Entropy 23, no. 6 (June 5, 2021): 720. http://dx.doi.org/10.3390/e23060720.
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With the use of thermodynamics and general equilibrium conditions only, we study the entropy of a fluid in the vicinity of the critical point of the liquid–vapor phase transition. By assuming a general form for the coexistence curve in the vicinity of the critical point, we show that the functional dependence of the entropy as a function of energy and particle densities necessarily obeys the scaling form hypothesized by Widom. Our analysis allows for a discussion of the properties of the corresponding scaling function, with the interesting prediction that the critical isotherm has the same functional dependence, between the energy and the number of particles densities, as the coexistence curve. In addition to the derivation of the expected equalities of the critical exponents, the conditions that lead to scaling also imply that, while the specific heat at constant volume can diverge at the critical point, the isothermal compressibility must do so.
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Yu, Xinting, Yue Yu, Julia Garver, Jialin Li, Abigale Hawthorn, Ella Sciamma-O’Brien, Xi Zhang, and Erika Barth. "Material Properties of Organic Liquids, Ices, and Hazes on Titan." Astrophysical Journal Supplement Series 266, no. 2 (June 1, 2023): 30. http://dx.doi.org/10.3847/1538-4365/acc6cf.
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Abstract Titan has a diverse range of materials in its atmosphere and on its surface: the simple organics that reside in various phases (gas, liquid, and ice) and the solid complex refractory organics that form Titan’s haze layers. These materials all actively participate in various physical processes on Titan, and many material properties are found to be important in shaping these processes. Future in situ explorations on Titan would likely encounter a range of materials, and a comprehensive database to archive the material properties of all possible material candidates will be needed. Here, we summarize several important material properties of the organic liquids, ices, and the refractory hazes on Titan that are available in the literature and/or that we have computed. These properties include thermodynamic properties (phase-change points, sublimation and vaporization saturation vapor pressure, and latent heat), and physical properties (organic liquid densities and organic ice and haze densities). We have developed a new database to provide a repository for these data and make them available to the science community. These data can be used as inputs for various theoretical models to interpret current and future remote sensing and in situ atmospheric and surface measurements on Titan. The material properties of the simple organics may also be applicable to giant planets and icy bodies in the outer solar system, interstellar medium, protoplanetary disks, and exoplanets.
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Safonov, O. G., L. Bindi, and V. L. Vinograd. "Potassium-bearing clinopyroxene: a review of experimental, crystal chemical and thermodynamic data with petrological applications." Mineralogical Magazine 75, no. 4 (August 2011): 2467–84. http://dx.doi.org/10.1180/minmag.2011.075.4.2467.
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AbstractAvailable experimental data on chemical composition and crystal structure of K-bearing clinopyroxenes are compiled together with the results of atomistic simulations and thermodynamic calculations of mineral equilibria. It is shown that the limited solubility of K2O in clinopyroxene from crustal rocks cannot be ascribed to the strong non-ideality of mixing between diopside (CaMgSi2O6) and K-jadeite (KAlSi2O6) components. The more likely reason is the instability of the potassic endmember with respect to other K-bearing phases. As the volume effects of typical K-jadeite-forming reactions are negative, the incorporation of K in the clinopyroxene structure becomes less difficult at higher pressure. Atomistic simulations predict that the thermodynamic mixing properties of diopside-K-jadeite solid-solutions at high temperature approach those of a regular mixture with a relatively small positive excess enthalpy. The standard enthalpy of formation (ΔfH° = —2932.7 kJ/mol), the standard volume (V° = 6.479 J mol–1 bar–1) and the isothermal bulk modulus (K0 = 145 GPa) of K-jadeite were calculated from first principles, and the standard entropy (S° = 141.24 J mol–1 K–1) and thermal-expansion coefficient (α = 3.3 x 1CP–5 K–1) of the K-jadeite endmember were estimated using quasi-harmonic lattice-dynamic calculations based on a force-field model. The estimated thermodynamic data are used to compute compositions of K-bearing clinopyroxenes in diverse mineral assemblages within a wide P-T interval. The review substantiates the conclusion that clinopyroxene can serve as an effective container for K at upper-mantle conditions.
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Mehboob, Muhammad Yasir, Riaz Hussain, Zobia Irshad, Ume Farwa, Muhammad Adnan, and Shabbir Muhammad. "Designing and Encapsulation of Inorganic Al12N12 Nanoclusters with Be, Mg, and Ca Metals for Efficient Hydrogen Adsorption: A Step Forward Towards Hydrogen Storage Materials." Journal of Computational Biophysics and Chemistry 20, no. 07 (October 7, 2021): 687–705. http://dx.doi.org/10.1142/s2737416521500411.
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Nanoclusters such as [Formula: see text][Formula: see text] have received increased attention due to their diverse applications in the fields of optoelectronics and energy storage. In this paper, we have investigated a series of alkaline earth metal (AEM)-encapsulated [Formula: see text][Formula: see text] nanoclusters for hydrogen adsorption. Thermodynamic adsorption parameters, optical and nonlinear optical properties were investigated using density functional theory (DFT) at the B3LYP/6-31G(d,p) level of theory. Encapsulation of AEMs (Be, Mg and Ca) is an effective strategy to improve the NLO reaction and thermodynamic and adsorption properties of [Formula: see text][Formula: see text] nanoclusters. The adsorption energies ranging from [Formula: see text]26.57[Formula: see text]kJ/mol to [Formula: see text]213.33[Formula: see text]kJ/mol for the three guests (Be, Mg and Ca) capsulated [Formula: see text][Formula: see text] nanoclusters are observed. The adsorption energy is affected by the size of the nanocage. Therefore, Ca- and Mg-encapsulated cages show higher values of adsorption energy. Overall, an increase in adsorption energy ([Formula: see text][Formula: see text]kJ/mol to [Formula: see text]91.06[Formula: see text]kJ/mol) is observed for (Be, Mg and Ca) encapsulated [Formula: see text][Formula: see text] nanoclusters compared to untreated [Formula: see text][Formula: see text] and H2-[Formula: see text][Formula: see text] cages. Moreover, adsorption of hydrogen on AEMs encapsulated in [Formula: see text][Formula: see text] leads to a decrease in the HOMO-LUMO energy gap with an enhancement of linear and nonlinear hyperpolarizability. All hydrogen-adsorbed AEMs [Formula: see text][Formula: see text] nanocages exhibit large [Formula: see text] and [Formula: see text] values, suggesting that these systems are potential candidates for optical materials. Various geometrical parameters such as frontier molecular orbitals (FMOs), partial density of states, global quantum descriptor of reactivity, natural bond orbital testing and molecular electrostatic strength analyses were performed to investigate the thermodynamic stability of all the studied systems. The results obtained confirmed that the designed systems are suitable for hydrogen storage. Therefore, we recommend that these systems be investigated for their hydrogen storage and optical properties.
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Frolova, Yuliya, Varuzhan Sarkisyan, Roman Sobolev, Mariia Makarenko, Michael Semin, and Alla Kochetkova. "The Influence of Edible Oils’ Composition on the Properties of Beeswax-Based Oleogels." Gels 8, no. 1 (January 9, 2022): 48. http://dx.doi.org/10.3390/gels8010048.
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This study aimed to find relationships between the properties of beeswax-based oleogels and the type of oil used. The influence of linseed, sunflower, olive, and fish oils was studied. For these oils, the fatty acid composition, the content of total polar components, and the iodine value were characterized. Textural and thermodynamic properties were determined for oleogels, the oil-binding capacity was estimated, and the morphology of crystals was studied. The concentration of beeswax in all oleogels was 6.0% w/w. It was shown that the type of oil has a significant influence on all characteristics of the oleogels. The use of different oils at the same technological treatment leads to the formation of crystals of diverse morphology—from platelets to spherulites. At the same time, it was revealed that some characteristics of oils have a varying contribution to the properties of oleogels. The content of total polar materials in oils is associated with a decrease in strength parameters (yield value and elastic modulus) and the oil-binding capacity of oleogels. In its turn, the iodine value of oils has a close positive correlation with the melting and crystallization temperatures of oleogels. The results obtained in this article indicate that the properties of beeswax-based oleogels can be directed by changing the oil composition.
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Kourki, Hajir, Mohammad Hossein Navid Famili, Mehrzad Mortezaei, and Milad Malekipirbazari. "Mixing challenges for SiO2/polystyrene nanocomposites." Journal of Thermoplastic Composite Materials 31, no. 5 (July 12, 2017): 709–26. http://dx.doi.org/10.1177/0892705717718599.
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Morphology of a nanocomposite, which has indisputable effects on its properties, is determined by its dynamic and thermodynamic conditions. While physical properties of the components of a nanocomposite as well as the interaction between them are the parameters controlling the morphology thermodynamically, their dynamic condition is related to the issues like intensity of mixing and geometry of mixer. In this research, we investigate the mixing process of solution casting method by studying the effects of mixing intensity on the dynamics of the particle structure and hereby its morphology using sedimentation test. In these experiments, mixing is performed at various durations, input energies, and energy types for suspensions containing different particle sizes and concentrations as well as diverse polymer concentrations. We found that increasing mixing time and input energy along with using ultrasonic wave decrease the size of aggregates. Sedimentation test revealed improvements of dispersion and distribution states of suspension by using ultrasonic waves and high shear mixing, respectively. Finally, particle–particle interaction data show increase in the probability of restructuring after mixing with reduction in particle size and increase in particle volume fraction.
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Dear, Alexander J., Thomas C. T. Michaels, Georg Meisl, David Klenerman, Si Wu, Sarah Perrett, Sara Linse, Christopher M. Dobson, and Tuomas P. J. Knowles. "Kinetic diversity of amyloid oligomers." Proceedings of the National Academy of Sciences 117, no. 22 (May 15, 2020): 12087–94. http://dx.doi.org/10.1073/pnas.1922267117.
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The spontaneous assembly of proteins into amyloid fibrils is a phenomenon central to many increasingly common and currently incurable human disorders, including Alzheimer’s and Parkinson’s diseases. Oligomeric species form transiently during this process and not only act as essential intermediates in the assembly of new filaments but also represent major pathogenic agents in these diseases. While amyloid fibrils possess a common, defining set of physicochemical features, oligomers, by contrast, appear much more diverse, and their commonalities and differences have hitherto remained largely unexplored. Here, we use the framework of chemical kinetics to investigate their dynamical properties. By fitting experimental data for several unrelated amyloidogenic systems to newly derived mechanistic models, we find that oligomers present with a remarkably wide range of kinetic and thermodynamic stabilities but that they possess two properties that are generic: they are overwhelmingly nonfibrillar, and they predominantly dissociate back to monomers rather than maturing into fibrillar species. These discoveries change our understanding of the relationship between amyloid oligomers and amyloid fibrils and have important implications for the nature of their cellular toxicity.
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Ciro, Yhors, John Rojas, Cristian J. Yarce, and Constain H. Salamanca. "Production and Characterization of Glutathione-Chitosan Conjugate Films as Systems for Localized Release of Methotrexate." Polymers 11, no. 12 (December 7, 2019): 2032. http://dx.doi.org/10.3390/polym11122032.
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Cancer is one of the most serious public health problems that affect humanity. Diverse delivery systems of anticancer drugs have been developed to enhance the treatment effectiveness and patient compliance. Thus, drug delivery systems from polymeric films could be an interesting and promising alternative, especially for skin chemotherapeutics. In this work, polymeric films based on glutathione-chitosan conjugates with degrees of thiolation of 4.4%, 5.1% and 7.0% were synthetized by casting-evaporation method and subsequent loading with methotrexate. The surface properties of these films were evaluated by contact angle and spreading rate measurements. The sessile drop methods along with the thermodynamic parameter of work of adhesion were determined using the Young–Dupré semi-empirical model. The in vitro methotrexate release was assessed at a pH of 4.5 and 7.4 simulating physiological conditions. Data from the resulting profiles were fitted to the order one, Higuchi, Peppas–Sahlin and Korsmeyer–Peppas kinetic models. The results suggest a strong relationship between the thiolation degree and hydrophilic surface properties such as contact angle and water spreading rate, whereas the work of adhesion was not significantly affected. Further, these polymer films could control the methotrexate release through diverse mechanisms such as diffusion and relaxation depending on the thiolation degree and the aqueous medium employed. In fact, as thiolation degree increased, the release mechanism shifted from a primary diffusional type towards a predominant relaxation-driven mechanism. These polymer films could be used as modified systems for anticancer local delivery.
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Poma, Adolfo B., Horacio V. Guzman, Mai Suan Li, and Panagiotis E. Theodorakis. "Mechanical and thermodynamic properties of Aβ42, Aβ40, and α-synuclein fibrils: a coarse-grained method to complement experimental studies." Beilstein Journal of Nanotechnology 10 (February 19, 2019): 500–513. http://dx.doi.org/10.3762/bjnano.10.51.
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We perform molecular dynamics simulation on several relevant biological fibrils associated with neurodegenerative diseases such as Aβ40, Aβ42, and α-synuclein systems to obtain a molecular understanding and interpretation of nanomechanical characterization experiments. The computational method is versatile and addresses a new subarea within the mechanical characterization of heterogeneous soft materials. We investigate both the elastic and thermodynamic properties of the biological fibrils in order to substantiate experimental nanomechanical characterization techniques that are quickly developing and reaching dynamic imaging with video rate capabilities. The computational method qualitatively reproduces results of experiments with biological fibrils, validating its use in extrapolation to macroscopic material properties. Our computational techniques can be used for the co-design of new experiments aiming to unveil nanomechanical properties of biological fibrils from a point of view of molecular understanding. Our approach allows a comparison of diverse elastic properties based on different deformations , i.e., tensile (Y L), shear (S), and indentation (Y T) deformation. From our analysis, we find a significant elastic anisotropy between axial and transverse directions (i.e., Y T > Y L) for all systems. Interestingly, our results indicate a higher mechanostability of Aβ42 fibrils compared to Aβ40, suggesting a significant correlation between mechanical stability and aggregation propensity (rate) in amyloid systems. That is, the higher the mechanical stability the faster the fibril formation. Finally, we find that α-synuclein fibrils are thermally less stable than β-amyloid fibrils. We anticipate that our molecular-level analysis of the mechanical response under different deformation conditions for the range of fibrils considered here will provide significant insights for the experimental observations.
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Maicas, Riki, Irena Yungerman, Yarden B. Weber, and Simcha Srebnik. "United-Atom Molecular Dynamics Study of the Mechanical and Thermomechanical Properties of an Industrial Epoxy." Polymers 13, no. 19 (October 8, 2021): 3443. http://dx.doi.org/10.3390/polym13193443.
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Epoxy resins are the most commonly used adhesives in industry due to their versatility, low cost, low toxicity, low shrinkage, high strength, resistance to moisture, and effective electrical resistance. These diverse properties can be tailored based on the chemical structure of the curing agent and the conditions of the curing process. Molecular simulations of epoxy resins have gained attention in recent years as a means to navigate the vast choice of chemical agents and conditions that will give the required properties of the resin. This work examines the statistical uncertainty in predicting thermodynamic and mechanical properties of an industrial epoxy resin using united atom molecular dynamics simulation. The results are compared with experimental measurements of the elastic modulus, Poisson’s ratio, and the glass transition temperature obtained at different temperatures and degrees of curing. The decreasing trend of the elastic modulus with increasing temperature is accurately captured by the simulated model, though the uncertainty in the calculated average is large. The glass transition temperature is expectedly overpredicted due to the high rates accessible to molecular simulations. We find that Poisson’s ratio is particularly sensitive to sample anisotropy as well as the method of evaluation, which explains the lack of consistent trends previously observed with molecular simulation at different degrees of crosslinking and temperatures.
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Bankole, Anifat Adenike, Vijo Poulose, Tholkappiyan Ramachandran, Fathalla Hamed, and Thies Thiemann. "Comparative Study of the Selective Sorption of Organic Dyes on Inorganic Materials—A Cost-Effective Method for Waste Treatment in Educational and Small Research Laboratories." Separations 9, no. 6 (June 7, 2022): 144. http://dx.doi.org/10.3390/separations9060144.
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Educational and research laboratories often produce relatively small amounts of highly diverse organic wastes. Treating waste can contribute significantly to the cost of running laboratories. This study introduced a simple and economical waste management system such that readily available used chromatography-grade inorganic materials, such as silica and alumina (basic and acidic), are utilized to treat remnant dye solutions and solution wastes from educational and small research laboratories. To recycle the adsorbents, they were heated to 600 °C, where the adsorbates were combusted. The results showed that acidic alumina is an effective adsorbent material for azo dyes and anionic dyes/stains, as well as textile dyes, with a 98 to 100% removal efficiency. Furthermore, alumina and silica possess excellent regeneration properties, where the dye removal efficiency of the materials was retained after regeneration at 600 °C. The adsorption properties of the materials were compared with those of aliginite and activated biomass from coffee grounds. Kinetic and thermodynamic studies of the sorption processes on the different materials were carried out. Overall, the inorganic materials used were efficient at removing contaminating remnant organic dyes stemming from educational and small research laboratories.
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Seaver, Samuel M. D., Filipe Liu, Qizhi Zhang, James Jeffryes, José P. Faria, Janaka N. Edirisinghe, Michael Mundy, et al. "The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes." Nucleic Acids Research 49, no. D1 (September 28, 2020): D575—D588. http://dx.doi.org/10.1093/nar/gkaa746.
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Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org/biochem and KBase.
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Azum, Naved, Malik Abdul Rub, Anish Khan, Maha M. Alotaibi, and Abdullah M. Asiri. "Synergistic Interaction and Binding Efficiency of Tetracaine Hydrochloride (Anesthetic Drug) with Anionic Surfactants in the Presence of NaCl Solution Using Surface Tension and UV–Visible Spectroscopic Methods." Gels 8, no. 4 (April 11, 2022): 234. http://dx.doi.org/10.3390/gels8040234.
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Surfactants are ubiquitous materials that are used in diverse formulations of various products. For instance, they improve the formulation of gel by improving its wetting and rheological properties. Here, we describe the effects of anionic surfactants on an anesthetic drug, tetracaine hydrochloride (TCH), in NaCl solution with tensiometry and UV–visible techniques. Various micellar, interfacial, and thermodynamic parameters were estimated. The outputs were examined by using different theoretical models to attain a profound knowledge of drug–surfactant mixtures. The presence of attractive interactions among drug and surfactant monomers (synergism) in mixed micelle was inferred. However, it was found that sodium dodecyl sulfate (SDS) showed greater interactions with the drug in comparison to sodium lauryl sarcosine (SLS). The binding of the drug with surfactants was monitored with a spectroscopic technique (UV–visible spectra). The results of this study could help optimize the compositions of these mixed aggregates and find the synergism between monomers of different used amphiphiles.
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Adeyemi, O. S., A. F. Sulaiman, and O. M. Iniaghe. "Interaction between Gallotannin and a Recombinant Form of Arginine Kinase of Trypanosoma brucei: Thermodynamic and Spectrofluorimetric Evaluation." Journal of Biophysics 2014 (August 26, 2014): 1–7. http://dx.doi.org/10.1155/2014/675905.
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Current chemotherapies against trypanosomiasis are beset with diverse challenges, a situation which underscores the numerous research efforts aimed at finding newer and effective treatments. Arginine kinase of trypanosome has been validated as target for drug development against trypanosomiasis. The present study investigated the interaction between a recombinant form of the arginine kinase (rTbAK) of trypanosome and gallotannin. The interaction between gallotannin and recombinant arginine kinase of Trypanosoma brucei caused significant decrease of enzyme activity. Kinetic analysis revealed the interaction to be of noncompetitive inhibition. Further thermodynamic analysis showed that the interaction between gallotannin and the recombinant arginine kinase was nonspontaneous and involved hydrophobic forces. The Ksv values and the FRET analysis suggest that static quenching of fluorescence intensity by gallotannin was static. Data revealed inhibitory interactions between gallotannin and rTbAK of trypanosome. Although the mechanism of inhibition is not clear yet, molecular docking studies are ongoing to clearly define the inhibitory interactions between the gallotannin and rTbAK. The knowledge of such binding properties would enrich development of selective inhibitors for the arginine kinase of Trypanosoma brucei.
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Rogerson, M., H. M. Pedley, and A. Kelham. "Linking process and product in terrestrial carbonates using a solution thermodynamic approach." Earth Surface Dynamics Discussions 1, no. 1 (September 11, 2013): 337–85. http://dx.doi.org/10.5194/esurfd-1-337-2013.
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Abstract. Determining the processes which generate terrestrial carbonate deposits (tufas, travertines and associated chemical sediments) is a long-standing problem. Deposition of mineral products from solution reflects a complex combination of biological, equilibrium and kinetic processes, and the differences in products these processes produce are yet to be clearly demarked. Building on the groundbreaking work of previous authors, we propose that the underlying control on the processes leading to the deposition of these products can be most parsimoniously understood from the thermodynamic properties of their source solutions. Here, we report initial observations of the differences in product generated from spring and lake systems spanning a range of temperature : supersaturation space. We find that at high supersaturation, biological influences are masked by high rates of spontaneous nucleation and sedimentary products from these settings infrequently exhibit classic "biomediated" fabrics such as clotted micrite. Likewise, at high temperature exclusion of vascular plants and complex/diverse biofilms significantly inhibits the magnitude of biomediated precipitation, again impeding the likelihood of encountering the "bio-type" fabrics. Conversely, despite the clear division in product between extensive tufa facies associations and discontinuous deposits such as oncoid beds, no clear division can be identified between these systems in temperature : supersaturation space. We reiterate the conclusion of previous authors, which demonstrate that this division cannot be made on the basis of physico-chemical characteristics of the solution alone. We further provide a new case study of this division from two adjacent systems in the UK, where continuous tufa-like deposition is happening at a site with lower supersaturation than other sites exhibiting only discontinuous (oncoidal) deposition. However, a strong microbiological division is demonstrated between these sites on the basis of suspended bacterial cell distribution, which reach a prominent maximum where tufa-like deposits are forming. We conclude that at high supersaturation, the thermodynamic properties of solutions provide a highly satisfactory means of linking process and product, raising the opportunity of identifying water characteristics from sedimentological/petrological characteristics of ancient deposits. At low supersaturation, we recommend that future research focuses on geomicrobiological processes rather than the more traditional, inorganic solution chemistry approach dominant in the past.
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Ulrich, Anne S. "Biophysical Aspects of Using Liposomes as Delivery Vehicles." Bioscience Reports 22, no. 2 (April 1, 2002): 129–50. http://dx.doi.org/10.1023/a:1020178304031.
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Liposomes are used as biocompatible carriers of drugs, peptides, proteins, plasmic DNA, antisense oligonucleotides or ribozymes, for pharmaceutical, cosmetic, and biochemical purposes. The enormous versatility in particle size and in the physical parameters of the lipids affords an attractive potential for constructing tailor-made vehicles for a wide range of applications. Some of the recent literature will be reviewed here and presented from a biophysical point of view, thus providing a background for the more specialized articles in this special issue on liposome technology. Different properties (size, colloidal behavior, phase transitions, and polymorphism) of diverse lipid formulations (liposomes, lipoplexes, cubic phases, emulsions, and solid lipid nanoparticles) for distinct applications (parenteral, transdermal, pulmonary, and oral administration) will be rationalized in terms of common structural, thermodynamic and kinetic parameters of the lipids. This general biophysical basis helps to understand pharmaceutically relevant aspects such as liposome stability during storage and towards serum, the biodistribution and specific targeting of cargo, and how to trigger drug release and membrane fusion. Methods for the preparation and characterization of liposomal formulations in vitro will be outlined, too.