Journal articles: 'Minimum Energy Pathway'

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Philippe, T., and D. Blavette. "Minimum free-energy pathway of nucleation." Journal of Chemical Physics 135, no. 13 (October 7, 2011): 134508. http://dx.doi.org/10.1063/1.3644935.

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Shim, JaeHwan, Juyong Lee, and Jaejun Yu. "Efficient discovery of multiple minimum action pathways using Gaussian process." Journal of Physics Communications 7, no. 2 (February 1, 2023): 025004. http://dx.doi.org/10.1088/2399-6528/acba83.

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Abstract We present a new efficient transition pathway search method based on the least action principle and the Gaussian process regression method. Most pathway search methods developed so far rely on string representations, which approximate a transition pathway by a series of slowly varying system replicas. Such string methods are computationally expensive in general because they require many replicas to obtain smooth pathways. Here, we present an approach employing the Gaussian process regression method, which infers the shape of a potential energy surface with a few observed data and Gaussian-shaped kernel functions. We demonstrate a drastic elevation of computing efficiency of the method about five orders of magnitude than existing methods. Further, to demonstrate its real-world capabilities, we apply our method to find multiple conformational transition pathways of alanine dipeptide using a quantum mechanical potential. Owing to the improved efficiency of our method, Gaussian process action optimization (GPAO), we obtain the multiple transition pathways of alanine dipeptide and calculate their transition probabilities successfully with density-functional theory (DFT) accuracy. In addition, GPAO successfully finds the isomerization pathways of small molecules and the rearrangement of atoms on a metallic surface.

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Chen, D., W. Hu, F. Gao, H. Deng, and L. Sun. "Tungsten cluster migration on nanoparticles: minimum energy pathway and migration mechanism." European Physical Journal B 80, no. 1 (March 2011): 31–40. http://dx.doi.org/10.1140/epjb/e2011-10629-9.

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Borodin, Dmitriy, Igor Rahinov, Pranav R. Shirhatti, Meng Huang, Alexander Kandratsenka, Daniel J. Auerbach, Tianli Zhong, et al. "Following the microscopic pathway to adsorption through chemisorption and physisorption wells." Science 369, no. 6510 (September 17, 2020): 1461–65. http://dx.doi.org/10.1126/science.abc9581.

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Adsorption involves molecules colliding at the surface of a solid and losing their incidence energy by traversing a dynamical pathway to equilibrium. The interactions responsible for energy loss generally include both chemical bond formation (chemisorption) and nonbonding interactions (physisorption). In this work, we present experiments that revealed a quantitative energy landscape and the microscopic pathways underlying a molecule’s equilibration with a surface in a prototypical system: CO adsorption on Au(111). Although the minimum energy state was physisorbed, initial capture of the gas-phase molecule, dosed with an energetic molecular beam, was into a metastable chemisorption state. Subsequent thermal decay of the chemisorbed state led molecules to the physisorption minimum. We found, through detailed balance, that thermal adsorption into both binding states was important at all temperatures.

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Takizawa, Hiroki, Junichi Iwakiri, Goro Terai, and Kiyoshi Asai. "Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model." Bioinformatics 36, Supplement_1 (July 1, 2020): i227—i235. http://dx.doi.org/10.1093/bioinformatics/btaa469.

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Abstract Motivation RNA folding kinetics plays an important role in the biological functions of RNA molecules. An important goal in the investigation of the kinetic behavior of RNAs is to find the folding pathway with the lowest energy barrier. For this purpose, most of the existing methods use heuristics because the number of possible pathways is huge even if only the shortest (direct) folding pathways are considered. Results In this study, we propose a new method using a best-first search strategy to efficiently compute the exact solution of the minimum barrier energy of direct pathways. Using our method, we can find the exact direct pathways within a Hamming distance of 20, whereas the previous methods even miss the exact short pathways. Moreover, our method can be used to improve the pathways found by existing methods for exploring indirect pathways. Availability and implementation The source code and datasets created and used in this research are available at https://github.com/eukaryo/czno. Supplementary information Supplementary data are available at Bioinformatics online.

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Lee, Brian Hyun-jong, and Gaurav Arya. "Assembly mechanism of surface-functionalized nanocubes." Nanoscale 14, no. 10 (2022): 3917–28. http://dx.doi.org/10.1039/d1nr07995f.

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Schmelzer, Jürn W. P., and Alexander S. Abyzov. "Comment on “Minimum free-energy pathway of nucleation” [J. Chem. Phys. 135, 134508 (2011)]." Journal of Chemical Physics 136, no. 10 (March 14, 2012): 107101. http://dx.doi.org/10.1063/1.3692688.

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Hong, Young J., and Dean J. Tantillo. "The Variediene-Forming Carbocation Cyclization/Rearrangement Cascade." Australian Journal of Chemistry 70, no. 4 (2017): 362. http://dx.doi.org/10.1071/ch16504.

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An energetically viable (on the basis of results from density functional theory computations) pathway to the diterpene variediene is described. Only one of the three secondary carbocations along this pathway is predicted to be a minimum on the potential energy surface.

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Monferrer, Ezequiel, Isaac Vieco-Martí, Amparo López-Carrasco, Fernando Fariñas, Sergio Abanades, Luis de la Cruz-Merino, Rosa Noguera, and Tomás Álvaro Naranjo. "Metabolic Classification and Intervention Opportunities for Tumor Energy Dysfunction." Metabolites 11, no. 5 (April 23, 2021): 264. http://dx.doi.org/10.3390/metabo11050264.

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A comprehensive view of cell metabolism provides a new vision of cancer, conceptualized as tissue with cellular-altered metabolism and energetic dysfunction, which can shed light on pathophysiological mechanisms. Cancer is now considered a heterogeneous ecosystem, formed by tumor cells and the microenvironment, which is molecularly, phenotypically, and metabolically reprogrammable. A wealth of evidence confirms metabolic reprogramming activity as the minimum common denominator of cancer, grouping together a wide variety of aberrations that can affect any of the different metabolic pathways involved in cell physiology. This forms the basis for a new proposed classification of cancer according to the altered metabolic pathway(s) and degree of energy dysfunction. Enhanced understanding of the metabolic reprogramming pathways of fatty acids, amino acids, carbohydrates, hypoxia, and acidosis can bring about new therapeutic intervention possibilities from a metabolic perspective of cancer.

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Singh, Baltej, Mayanak Kumar Gupta, Ranjan Mittal, Mohamed Zbiri, Stephane Rols, Sadequa Jahedkhan Patwe, Srungarpu Nagabhusan Achary, Helmut Schober, Avesh Kumar Tyagi, and Samrath Lal Chaplot. "Superionic conduction in β-eucryptite: inelastic neutron scattering and computational studies." Physical Chemistry Chemical Physics 19, no. 23 (2017): 15512–20. http://dx.doi.org/10.1039/c7cp01490b.

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Yanamandra, Kaushik, Rakesh K. Behera, Atef Daoud, and Nikhil Gupta. "Migration Barrier Estimation of Carbon in Lead for Lead–Acid Battery Applications: A Density Functional Theory Approach." Solids 3, no. 2 (March 22, 2022): 177–87. http://dx.doi.org/10.3390/solids3020012.

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Recent efforts towards developing novel lead electrodes involving carbon and lead composites have shown potential for increasing the cycle life of lead–acid (LA) batteries used to store energy in various applications. In this study, first-principles calculations are used to examine the structural stability, defect formation energy, and migration barrier of C in Pb for LA batteries. Density functional theory with the GGA-PBE functional performed the best out of various functionals used for structural stability calculations. Furthermore, with the complete incorporation of C in the Pb matrix, the results show that C is energetically preferred to be at the octahedral interstitial (CiOcta) site in the FCC structure of Pb. Additionally, climbing-image nudged elastic band calculations show a minimum energy pathway for C diffusing from a stable octahedral site to the adjacent octahedral site assisted by a tetrahedral intermediate site. Therefore, the minimum energy pathway for C migration is envisioned to be CiOcta→ CiTetra→CiOcta, where the total energy barrier is observed to be ~90% and more than 100% lower than the CiTetra→CiTetra and CiOcta→CiOcta barriers, respectively.

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Lu, Yanxia, Qing Peng, and Chenguang Liu. "Ab Initio Investigation of Helium Mobility in La2Zr2O7 Pyrochlore." Crystals 11, no. 6 (June 10, 2021): 667. http://dx.doi.org/10.3390/cryst11060667.

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The α-decay of incorporated actinides continuously produces helium, resulting in helium accumulation and causing security concerns for nuclear waste forms. The helium mobility is a key issue affecting the accumulation and kinetics of helium. The energy barriers and migration pathways of helium in a potential high-level nuclear waste forms, La2Zr2O7 pyrochlore, have been investigated in this work using the climbing image nudged elastic band method with density functional theory. The minimum energy pathway for helium to migrate in La2Zr2O7 is identified as via La–La interstitial sites with a barrier of 0.46 eV. This work may offer a theoretical foundation for further prospective studies of nuclear waste forms.

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Yamamoto, Norifumi, Nobuaki Koga, and Masataka Nagaoka. "Ferryl–Oxo Species Produced from Fenton’s Reagent via a Two-Step Pathway: Minimum Free-Energy Path Analysis." Journal of Physical Chemistry B 116, no. 48 (November 27, 2012): 14178–82. http://dx.doi.org/10.1021/jp310008z.

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14

Zhu, Ting, Ju Li, and Sidney Yip. "Nanomechanics of Crack Front Mobility." Journal of Applied Mechanics 72, no. 6 (October 5, 2005): 932–35. http://dx.doi.org/10.1115/1.2047607.

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Minimum energy paths for unit advancement of a crack front are determined by reaction pathway sampling, thus providing the reaction coordinates for the analysis of crack tip mechanics in ductile and brittle materials. We compare results on activation energy barrier and atomic displacement distributions for an atomically sharp crack in Cu, where one observes the emission of a partial dislocation loop, and in Si, where crack front extension evolves in a kink-like fashion.

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Sugimura, Natsuhiko, Yoko Igarashi, Reiko Aoyama, and Toshimichi Shibue. "Nudged elastic band method and density functional theory calculation for finding a local minimum energy pathway of p-benzoquinone and phenol fragmentation in mass spectrometry." European Journal of Mass Spectrometry 23, no. 1 (February 2017): 40–44. http://dx.doi.org/10.1177/1469066716688412.

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Analysis of the fragmentation pathways of molecules in mass spectrometry gives a fundamental insight into gas-phase ion chemistry. However, the conventional intrinsic reaction coordinates method requires knowledge of the transition states of ion structures in the fragmentation pathways. Herein, we use the nudged elastic band method, using only the initial and final state ion structures in the fragmentation pathways, and report the advantages and limitations of the method. We found a minimum energy path of p-benzoquinone ion fragmentation with two saddle points and one intermediate structure. The primary energy barrier, which corresponded to the cleavage of the C–C bond adjacent to the CO group, was calculated to be 1.50 eV. An additional energy barrier, which corresponded to the cleavage of the CO group, was calculated to be 0.68 eV. We also found an energy barrier of 3.00 eV, which was the rate determining step of the keto-enol tautomerization in CO elimination from the molecular ion of phenol. The nudged elastic band method allowed the determination of a minimum energy path using only the initial and final state ion structures in the fragmentation pathways, and it provided faster than the conventional intrinsic reaction coordinates method. In addition, this method was found to be effective in the analysis of the charge structures of the molecules during the fragmentation in mass spectrometry.

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Digiesi, Salvatore, Giovanni Mummolo, and Micaela Vitti. "Minimum Emissions Configuration of a Green Energy–Steel System: An Analytical Model." Energies 15, no. 9 (May 3, 2022): 3324. http://dx.doi.org/10.3390/en15093324.

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The need to significantly reduce emissions from the steelmaking sector requires effective and ready-to-use technical solutions. With this aim, different decarbonization strategies have been investigated by both researchers and practitioners. To this concern, the most promising pathway is represented by the replacement of natural gas with pure hydrogen in the direct reduced iron (DRI) production process to feed an electric arc furnace (EAF). This solution allows to significantly reduce direct emissions of carbon dioxide from the DRI process but requires a significant amount of electricity to power electrolyzers adopted to produce hydrogen. The adoption of renewable electricity sources (green hydrogen) would reduce emissions by 95–100% compared to the blast furnace–basic oxygen furnace (BF–BOF) route. In this work, an analytical model for the identification of the minimum emission configuration of a green energy–steel system consisting of a secondary route supported by a DRI production process and a renewable energy conversion system is proposed. In the model, both technological features of the hydrogen steel plant and renewable energy production potential of the site where it is to be located are considered. Compared to previous studies, the novelty of this work consists of the joint modeling of a renewable energy system and a steel plant. This allows to optimize the overall system from an environmental point of view, considering the availability of green hydrogen as an inherent part of the model. Numerical experiments proved the effectiveness of the model proposed in evaluating the suitability of using green hydrogen in the steelmaking process. Depending on the characteristics of the site and the renewable energy conversion system adopted, decreases in emissions ranging from 60% to 91%, compared to the BF–BOF route, were observed for the green energy–steel system considered It was found that the environmental benefit of using hydrogen in the secondary route is strictly related to the national energy mix and to the electrolyzers’ technology. Depending on the reference context, it was found that there exists a maximum value of the emission factor from the national electricity grid below which is environmentally convenient to produce DRI by using only hydrogen. It was moreover found that the lower the electricity consumption of the electrolyzer, the higher the value assumed by the emission factor from the electricity grid, which makes the use of hydrogen convenient.

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Starling, S., D. Sanders, R. Kemp, and N. Haywood. "PATHWAY TO PETROLEUM—EASING SKILL SHORTAGES THROUGH AN INDUSTRY INDUCTION PROGRAM." APPEA Journal 46, no. 1 (2006): 587. http://dx.doi.org/10.1071/aj05039.

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To provide a pathway to employment, petroleum industry employers are sponsoring a standard induction program, delivered through a national network of training centres, which will be recognised as a passport for workers to gain access to oil and gas facilities.The Australian upstream petroleum industry faces many staffing challenges including: difficulties recruiting staff for new developments, competition from overseas projects for construction contractors, and the imminent retirement of an aging workforce. This growing employment demand and limited labour supply has created a strong competitive recruitment market that is characterised by skills shortages. Consequently, the industry is having to recruit workers from non-traditional labour pools and engage contractors whose workforce has limited oil and gas experience. Many of these workers are not familiar with petroleum industry processes, safety procedures, or environmental hazards.APPEA is supporting the development of the Induction Program to raise awareness and commence acquisition of these petroleum industry competencies; to facilitate wider staff recruitment; to up-skill contractors’ workforces; and, reduce repeated induction training while ensuring safety standards are maintained. The Induction Program will establish a qualification underpinned by a competency- based approach that is recognised as the minimum standard of entry level training for all workers in upstream petroleum workplaces. The Induction Program will be delivered through a national network of purpose-built Induction Centres designed to provide practical hands-on training in a simulated workplace environment.

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Zhang, Yanjun, and Shengyou Huang. "Exploring the Binding Mechanism and Dynamics of EndoMS/NucS to Mismatched dsDNA." International Journal of Molecular Sciences 20, no. 20 (October 17, 2019): 5142. http://dx.doi.org/10.3390/ijms20205142.

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The well-known mismatch repair (MMR) machinery, MutS/MutL, is absent in numerous Archaea and some Bacteria. Recent studies have shown that EndoMS/NucS has the ability to cleave double-stranded DNA (dsDNA) containing a mismatched base pair, which suggests a novel mismatch repair process. However, the recognition mechanism and the binding process of EndoMS/NucS in the MMR pathway remain unclear. In this study, we investigate the binding dynamics of EndoMS/NucS to mismatched dsDNA and its energy as a function of the angle between the two C-terminal domains of EndoMS/NucS, through molecular docking and extensive molecular dynamics (MD) simulations. It is found that there exists a half-open transition state corresponding to an energy barrier (at an activation angle of approximately 80 ∘ ) between the open state and the closed state, according to the energy curve. When the angle is larger than the activation angle, the C-terminal domains can move freely and tend to change to the open state (local energy minimum). Otherwise, the C-terminal domains will interact with the mismatched dsDNA directly and converge to the closed state at the global energy minimum. As such, this two-state system enables the exposed N-terminal domains of EndoMS/NucS to recognize mismatched dsDNA during the open state and then stabilize the binding of the C-terminal domains of EndoMS/NucS to the mismatched dsDNA during the closed state. We also investigate how the EndoMS/NucS recognizes and binds to mismatched dsDNA, as well as the effects of K + ions. The results provide insights into the recognition and binding mechanisms of EndoMS/NucS to mismatched dsDNA in the MMR pathway.

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Fang, Huang, Michael F. Hagan, and W. Benjamin Rogers. "Two-step crystallization and solid–solid transitions in binary colloidal mixtures." Proceedings of the National Academy of Sciences 117, no. 45 (October 29, 2020): 27927–33. http://dx.doi.org/10.1073/pnas.2008561117.

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Crystallization is fundamental to materials science and is central to a variety of applications, ranging from the fabrication of silicon wafers for microelectronics to the determination of protein structures. The basic picture is that a crystal nucleates from a homogeneous fluid by a spontaneous fluctuation that kicks the system over a single free-energy barrier. However, it is becoming apparent that nucleation is often more complicated than this simple picture and, instead, can proceed via multiple transformations of metastable structures along the pathway to the thermodynamic minimum. In this article, we observe, characterize, and model crystallization pathways using DNA-coated colloids. We use optical microscopy to investigate the crystallization of a binary colloidal mixture with single-particle resolution. We observe classical one-step pathways and nonclassical two-step pathways that proceed via a solid–solid transformation of a crystal intermediate. We also use enhanced sampling to compute the free-energy landscapes corresponding to our experiments and show that both one- and two-step pathways are driven by thermodynamics alone. Specifically, the two-step solid–solid transition is governed by a competition between two different crystal phases with free energies that depend on the crystal size. These results extend our understanding of available pathways to crystallization, by showing that size-dependent thermodynamic forces can produce pathways with multiple crystal phases that interconvert without free-energy barriers and could provide approaches to controlling the self-assembly of materials made from colloids.

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Cruzeiro, Leonor. "The VES KM: a pathway for protein folding in vivo." Pure and Applied Chemistry 92, no. 1 (January 28, 2020): 179–91. http://dx.doi.org/10.1515/pac-2019-0301.

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AbstractWhile according to the thermodynamic hypothesis, protein folding reproducibility is ensured by the assumption that the native state corresponds to the minimum of the free energy in normal cellular conditions, here, the VES kinetic mechanism for folding in vivo is described according to which the nascent chain of all proteins is helical and the first and structure defining step in the folding pathway is the bending of that initial helix around a particular amino acid site. Molecular dynamics simulations are presented which indicate both the viability of this mechanism for folding and its limitations in the presence of a Markovian thermal bath. An analysis of a set of protein structures formed only of helices and loops suggests that bending sites are correlated with regions bounded, on the N-side, by positively charged amino acids like Lysine and Histidine and on the C-side by negatively charged amino acids like Aspartic acid.

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Todorova, Teodora, Daniel Peitz, Oliver Kröcher, Alexander Wokaun, and Bernard Delley. "Guanidinium Formate Decomposition on the (101) TiO2-Anatase Surface: Combined Minimum Energy Reaction Pathway Calculations and Temperature-Programmed Decomposition Experiments." Journal of Physical Chemistry C 115, no. 4 (December 2010): 1195–203. http://dx.doi.org/10.1021/jp106523b.

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Zivieri, Roberto, and Nicola Pacini. "Entropy Density Acceleration and Minimum Dissipation Principle: Correlation with Heat and Matter Transfer in Glucose Catabolism." Entropy 20, no. 12 (December 5, 2018): 929. http://dx.doi.org/10.3390/e20120929.

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The heat and matter transfer during glucose catabolism in living systems and their relation with entropy production are a challenging subject of the classical thermodynamics applied to biology. In this respect, an analogy between mechanics and thermodynamics has been performed via the definition of the entropy density acceleration expressed by the time derivative of the rate of entropy density and related to heat and matter transfer in minimum living systems. Cells are regarded as open thermodynamic systems that exchange heat and matter resulting from irreversible processes with the intercellular environment. Prigogine’s minimum energy dissipation principle is reformulated using the notion of entropy density acceleration applied to glucose catabolism. It is shown that, for out-of-equilibrium states, the calculated entropy density acceleration for a single cell is finite and negative and approaches as a function of time a zero value at global thermodynamic equilibrium for heat and matter transfer independently of the cell type and the metabolic pathway. These results could be important for a deeper understanding of entropy generation and its correlation with heat transfer in cell biology with special regard to glucose catabolism representing the prototype of irreversible reactions and a crucial metabolic pathway in stem cells and cancer stem cells.

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Navarro-Retamal, Carlos, Stephan Schott-Verdugo, Holger Gohlke, and Ingo Dreyer. "Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway." International Journal of Molecular Sciences 22, no. 19 (September 26, 2021): 10345. http://dx.doi.org/10.3390/ijms221910345.

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Two Pore Channels (TPCs) are cation-selective voltage- and ligand-gated ion channels in membranes of intracellular organelles of eukaryotic cells. In plants, the TPC1 subtype forms the slowly activating vacuolar (SV) channel, the most dominant ion channel in the vacuolar membrane. Controversial reports about the permeability properties of plant SV channels fueled speculations about the physiological roles of this channel type. TPC1 is thought to have high Ca2+ permeability, a conclusion derived from relative permeability analyses using the Goldman–Hodgkin–Katz (GHK) equation. Here, we investigated in computational analyses the properties of the permeation pathway of TPC1 from Arabidopsis thaliana. Using the crystal structure of AtTPC1, protein modeling, molecular dynamics (MD) simulations, and free energy calculations, we identified a free energy minimum for Ca2+, but not for K+, at the luminal side next to the selectivity filter. Residues D269 and E637 coordinate in particular Ca2+ as demonstrated in in silico mutagenesis experiments. Such a Ca2+-specific coordination site in the pore explains contradicting data for the relative Ca2+/K+ permeability and strongly suggests that the Ca2+ permeability of SV channels is largely overestimated from relative permeability analyses. This conclusion was further supported by in silico electrophysiological studies showing a remarkable permeation of K+ but not Ca2+ through the open channel.

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Kim, Young-Kyu, Bum-Goo Cho, Soon-Yeol Park, and Taeyoung Won. "Ab-Initio Study of Neutral Indium Diffusion in Uniaxially- and Biaxially-Strained Silicon." Journal of Nanoscience and Nanotechnology 8, no. 9 (September 1, 2008): 4565–68. http://dx.doi.org/10.1166/jnn.2008.ic41.

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In this paper, we present our ab-initio study on energy configurations, minimum energy path (MEP), and migration energy for neutral indium diffusion in a uniaxial and biaxial tensile strained {100} silicon layer. Our ab-initio calculation of the electronic structure allowed us to figure out transient atomistic configurations during the indium diffusion in strained silicon. We found that the lowest-energy structure (Ins – SiiTd) consists of indium sitting on a substitutional site while stabilizing a silicon self-interstitial in a nearby tetrahedral position. Our ab-initio calculation implied that the next lowest energy structure is IniTd, the interstitial indium at the tetrahedral position. We employed the nudged elastic band (NEB) method for estimating the MEP between the two structures. The NEB method allowed us to find that that diffusion pathway of neutral indium is kept unchanged in strained silicon while the migration energy of indium fluctuates in strained silicon.

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Chen, Li An, Xing Feng Zhu, and Ling Fu Chen. "First principles investigation of the diffusion of interstitial Cu, Ag and Au in ZnTe." International Journal of Modern Physics B 29, no. 19 (July 21, 2015): 1550130. http://dx.doi.org/10.1142/s0217979215501301.

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The diffusion is of great significance in many applications when the impurities are employed to tune the semiconductor's electrical or optical properties. It is necessary to understand how dopant defects diffuse in semiconductors. Using first-principles calculations, we consider interstitial diffusion mechanisms and calculate the migration barrier energies of interstitial Cu, Ag and Au atoms in II–VI compounds ZnTe. We find that the relative size of dopant and bulk atoms is an important factor which affects the diffusion behavior. The high symmetry Tc site, which is tetrahedrally coordinated by four cation atoms, is the global minimum energy location for Ag and Au interstitials. The size of Cu adatom is small, so Cu is more stable when it locates at the Ta site which is tetrahedrally coordinated by four anion atoms. But the global minimum energy location for Cu interstitials is M site which is of smaller space than Ta. Cu adatoms show an asymmetric curve of energy diffusion barrier with two energetically distinct extremum in the pathway. Ag diffuses along nearly straight line paths along [111] or equivalent directions. Diffusion for Cu or Au deviates from the straight line paths along 〈111〉 avoiding high symmetric sites.

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Qiao, Qing-An, Yueqing Jin, Zhengting Cai, Rongjun Qu, Chuanlu Yang, and Meishan Wang. "Molecule dynamics and combined QM/MM study on one-carbon unit transfer reaction catalyzed by GAR transformylase." Open Chemistry 3, no. 4 (December 1, 2005): 674–82. http://dx.doi.org/10.2478/bf02475196.

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AbstractBoth a molecule dynamic study and a combined quantum mechanics and molecule mechanics (QM/MM) study on Glycinamide ribonucleotide transformylase (GAR Tfase) catalytic mechanism are presented. The results indicate a direct one-carbon unit transfer process but not a stepwise mechanism in this reaction. The residues near the active center can fix the cofactor (N10-formyltetrahydrofolate) and GAR in proper relative positions by a H-bond network. The transition state and the minimum energy pathway are located on the potential energy surface. After all the residues (including H2O molecules) are removed from the system the activation energy has increased from 145.1 kJ/mol to 243.3 kJ/mol, and the formly transfer reaction is very hard to achieve. The interactions between coenzyme, GAR and residues near the reactive center are discussed as well.

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Sarewicz, Marcin, Łukasz Bujnowicz, Satarupa Bhaduri, Sandeep K. Singh, William A. Cramer, and Artur Osyczka. "Metastable radical state, nonreactive with oxygen, is inherent to catalysis by respiratory and photosynthetic cytochromes bc1/b6f." Proceedings of the National Academy of Sciences 114, no. 6 (January 23, 2017): 1323–28. http://dx.doi.org/10.1073/pnas.1618840114.

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Oxygenic respiration and photosynthesis based on quinone redox reactions face a danger of wasteful energy dissipation by diversion of the productive electron transfer pathway through the generation of reactive oxygen species (ROS). Nevertheless, the widespread quinone oxido-reductases from the cytochrome bc family limit the amounts of released ROS to a low, perhaps just signaling, level through an as-yet-unknown mechanism. Here, we propose that a metastable radical state, nonreactive with oxygen, safely holds electrons at a local energetic minimum during the oxidation of plastohydroquinone catalyzed by the chloroplast cytochrome b6f. This intermediate state is formed by interaction of a radical with a metal cofactor of a catalytic site. Modulation of its energy level on the energy landscape in photosynthetic vs. respiratory enzymes provides a possible mechanism to adjust electron transfer rates for efficient catalysis under different oxygen tensions.

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Sun, Qiao, Sufan Wang, Hong Zhang, Zhen Li, Christoph Pifisterer, Stefan Fischer, Shinko Nanbu, and Sean C. Smith. "Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle." Australian Journal of Chemistry 63, no. 3 (2010): 363. http://dx.doi.org/10.1071/ch09509.

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We present the results of a systematic series of constrained minimum energy pathway calculations on ground state potential energy surfaces, for a cluster model of the proton chain transfer that mediates the photocycle of the green fluorescent protein, as well as for a model including the solvated protein environment. The calculations vary in terms of the types of modes that are assumed to be capable of relaxing in concert with the movement of the protons and the results demonstrate that the nature and extent of dynamical relaxation has a substantive impact on the activation energy for the proton transfer. We discuss the implications of this in terms of currently available dynamical models and chemical rate theories that might be brought to bear on the kinetics of this important example of proton chain transfer in a biological system.

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Gourlaouen, Christophe, Carine Clavaguéra, Aude Marjolin, Jean-Philip Piquemal, and Jean-Pierre Dognon. "Understanding the structure and electronic properties of Th4+-water complexes." Canadian Journal of Chemistry 91, no. 9 (September 2013): 821–31. http://dx.doi.org/10.1139/cjc-2012-0546.

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We present a systematic quantum chemistry study of the [Th(H2O)n]4+ (n = 1 to 10) complexes to gain insight into their electronic structure and properties: the effect of the ligand distribution on the valence shells of the thorium(IV) ion is studied by means of the electron localization function (ELF) topological analysis. Particular care is given to the study of the mono-aqua complex both at its equilibrium geometry, using various tools such as energy decomposition analyses (EDA), and along its dissociation pathway. Indeed, as several electronic states cross the Th4 +-H2O0 ground state along the minimum energy path, we demonstrate that the diabatic representation implemented in MOLPRO is able to generate reference potential energy surfaces that will lead to the evaluation of diabatic dissociation curves. The calculated diabatic interaction energy curve will allow for a consistent parameterization of new generation force fields dedicated to heavy metals based on quantum chemistry.

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Schafer, Nicholas P., Ha H. Truong, Daniel E. Otzen, Kresten Lindorff-Larsen, and Peter G. Wolynes. "Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease." Proceedings of the National Academy of Sciences 113, no. 8 (February 8, 2016): 2098–103. http://dx.doi.org/10.1073/pnas.1524027113.

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We investigate the folding of GlpG, an intramembrane protease, using perfectly funneled structure-based models that implicitly account for the absence or presence of the membrane. These two models are used to describe, respectively, folding in detergent micelles and folding within a bilayer, which effectively constrains GlpG's topology in unfolded and partially folded states. Structural free-energy landscape analysis shows that although the presence of multiple folding pathways is an intrinsic property of GlpG’s modular functional architecture, the large entropic cost of organizing helical bundles in the absence of the constraining bilayer leads to pathways that backtrack (i.e., local unfolding of previously folded substructures is required when moving from the unfolded to the folded state along the minimum free-energy pathway). This backtracking explains the experimental observation of thermodynamically destabilizing mutations that accelerate GlpG’s folding in detergent micelles. In contrast, backtracking is absent from the model when folding is constrained within a bilayer, the environment in which GlpG has evolved to fold. We also characterize a near-native state with a highly mobile transmembrane helix 5 (TM5) that is significantly populated under folding conditions when GlpG is embedded in a bilayer. Unbinding of TM5 from the rest of the structure exposes GlpG’s active site, consistent with studies of the catalytic mechanism of GlpG that suggest that TM5 serves as a substrate gate to the active site.

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Chan, Bun, and Leo Radom. "Modelling the Effect of Conformation on Hydrogen-Atom Abstraction from Peptides." Australian Journal of Chemistry 71, no. 4 (2018): 257. http://dx.doi.org/10.1071/ch17621.

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Computational quantum chemistry is used to examine the effect of conformation on the kinetics of hydrogen-atom abstraction by HO• from amides of glycine and proline as peptide models. In accord with previous findings, it is found that there are substantial variations possible in the conformations and the corresponding energies, with the captodative effect, hydrogen bonding, and solvation being some of the major features that contribute to the variations. The ‘minimum-energy-structure-pathway’ strategy that is often employed in theoretical studies of peptide chemistry with small models certainly provides valuable fundamental information. However, one may anticipate different reaction outcomes in structurally constrained systems due to modified reaction thermodynamics and kinetics, as demonstrated explicitly in the present study. Thus, using a ‘consistent-conformation-pathway’ approach may indeed be more informative in such circumstances, and in this regard theory provides information that would be difficult to obtain from experimental studies alone.

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Jadhaw, Arjun, and Vikrant Sharma. "AN IMPLEMENTATION OF EFFICIENT PATH SELECTION METHOD FOR SUCCESSFUL DATA TRANSMISSION IN MOBILE AD HOC NETWORKS." BSSS journal of computer 12, no. 1 (June 30, 2021): 36–48. http://dx.doi.org/10.51767/jc1205.

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Routing is a process of forwarding the data from a known source to the destination. In this procedure, the data might travel during some in-between paths, and there exist a required to select the best probable best possible nodes to forward the data. This best selection of nodes will permit to achieve a high presentation in the network. Big amount of worked has been carried out to find the best pathway in the network routing to progress its effectiveness and to eliminate overcrowding problems. A good routing algorithm should be able to find an optimal path and it must be simple. It also must have low overhead, and be robust and stable, converging rapidly, and must remain flexible. Routing in MANET by means of the direct pathway metric is not a sufficient situation to construct high quality pathway, since minimum hop count routing frequently chooses routes that have considerably less capacity than the best pathway that live in the network. In this article, we suggest a mechanism to prefer the routing protocol based on manifold measure like Throughput, PDR, energy expenditure etc. These paths are quite resourceful. Network presentation will be raise by using these paths. The efficiency of our mechanism is illustrated by simulations conducted using network simulator ns-2.

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Wang, Lin, Chiam Yu Ng, Satyakam Dash, and Costas D. Maranas. "Exploring the combinatorial space of complete pathways to chemicals." Biochemical Society Transactions 46, no. 3 (April 6, 2018): 513–22. http://dx.doi.org/10.1042/bst20170272.

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Computational pathway design tools often face the challenges of balancing the stoichiometry of co-metabolites and cofactors, and dealing with reaction rule utilization in a single workflow. To this end, we provide an overview of two complementary stoichiometry-based pathway design tools optStoic and novoStoic developed in our group to tackle these challenges. optStoic is designed to determine the stoichiometry of overall conversion first which optimizes a performance criterion (e.g. high carbon/energy efficiency) and ensures a comprehensive search of co-metabolites and cofactors. The procedure then identifies the minimum number of intervening reactions to connect the source and sink metabolites. We also further the pathway design procedure by expanding the search space to include both known and hypothetical reactions, represented by reaction rules, in a new tool termed novoStoic. Reaction rules are derived based on a mixed-integer linear programming (MILP) compatible reaction operator, which allow us to explore natural promiscuous enzymes, engineer candidate enzymes that are not already promiscuous as well as design de novo enzymes. The identified biochemical reaction rules then guide novoStoic to design routes that expand the currently known biotransformation space using a single MILP modeling procedure. We demonstrate the use of the two computational tools in pathway elucidation by designing novel synthetic routes for isobutanol.

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Zhang, Qiyan, Yawei Li, Haiyan Zhu, and Bingbing Suo. "High-Performance of Electrocatalytic CO2 Reduction on Defective Graphene-Supported Cu4S2 Cluster." Catalysts 12, no. 5 (April 19, 2022): 454. http://dx.doi.org/10.3390/catal12050454.

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Electrochemical CO2 reduction reaction (CO2RR) to high-value chemicals is one of the most splendid approaches to mitigating environmental threats and energy shortage. In this study, the catalytic performance of CO2RR on defective graphene-supported Cu4S2 clusters as well as isolated Cu4Xn (X = O, S, Se; n = 2, 4) was systematically investigated based on density functional theory (DFT) computations. Calculation results revealed that the most thermodynamically feasible product is CH3OH among the C1 products on Cu4X2 clusters, in which the Cu4S2 cluster has the best activity concerning CH3OH synthesis with a limiting potential of −0.48 V. When the Cu4S2 cluster was further supported on defective graphene, the strong interaction between cluster and substrate could greatly improve the performance via tuning the electronic structure and improving the stability of the Cu4S2 cluster. The calculated free energy diagram indicated that it is also more energetically preferable for CH3OH production with a low limiting potential of −0.35 V. Besides, the defective graphene support has a significant ability to suppress the competing reactions, such as the hydrogen evolution reaction (HER) and CO and HCOOH production. Geometric structures, limiting potentials, and reduction pathways were also discussed to gain insight into the reaction mechanism and to find the minimum-energy pathway for C1 products. We hope this work will provide theoretical reference for designing and developing advanced supported Cu-based electrocatalysts for CO2 reduction.

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Yamamoto, Norifumi, Genichi Sampei, and Gota Kawai. "Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase." Life 12, no. 2 (February 14, 2022): 281. http://dx.doi.org/10.3390/life12020281.

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The second step in the de novo biosynthetic pathway of purine is catalyzed by PurD, which consumes an ATP molecule to produce glycinamide ribonucleotide (GAR) from glycine and phosphoribosylamine (PRA). PurD initially reacts with ATP to produce an intermediate, glycyl-phosphate, which then reacts with PRA to produce GAR. The structure of the glycyl-phosphate intermediate bound to PurD has not been determined. Therefore, the detailed reaction mechanism at the molecular level is unclear. Here, we developed a computational protocol to analyze the free-energy profile for the glycine phosphorylation process catalyzed by PurD, which examines the free-energy change along a minimum energy path based on a perturbation method combined with the quantum mechanics and molecular mechanics hybrid model. Further analysis revealed that during the formation of glycyl-phosphate, the partial atomic charge distribution within the substrate molecules was not localized according to the formal charges, but was delocalized overall, which contributed significantly to the interaction with the charged amino acid residues in the ATP-grasp domain of PurD.

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Fujimoto, Kazushi, Motohiro Fukai, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, and Susumu Okazaki. "Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation." Pure and Applied Chemistry 92, no. 10 (October 25, 2020): 1585–94. http://dx.doi.org/10.1515/pac-2020-0109.

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AbstractEntecavir, triphosphorylated in liver cells, is an antiviral reagent against Hepatitis B virus (HBV). The reagent inhibits reverse transcription of RNA inside the virus capsid. In the present study, free energy profile of an Entecavir triphosphate (ETVTP) molecule has been calculated when it passes through pores of the capsid along two- and three-fold rotational symmetry axes in order to investigate permeation pathway of the reagent to the inside of the capsid. The calculations have been done based on thermodynamic integration (TI) method combined with all-atomistic molecular dynamic (MD) calculations. A free energy minimum of −19 kJ/mol was found at the entrance of the pore from the outside along the three-fold symmetry axis. This stabilization is from the interaction of negatively charged ETVTP with positively charged capsid methionine residues. This excess free energy concentrates of the reagent at the entrance of the pore by a factor of about 2000. A free energy barrier of approximately 13 kJ/mol was also found near the exit of the pore to the inside of the capsid due to narrow space of the pore surrounded by hydrophobic wall made by proline residues and negatively charged wall by aspartic acid residues. There, ETVTP is partially dehydrated in order to pass through the narrow space, which causes the great free energy loss. Further, the negatively charged residues produce repulsive forces on the ETVTP molecule. In contrast, in the case of the pore along the two-fold symmetry axis, the calculated free energy profile showed shallower free energy minimum, −4 kJ/mol at the entrance in spite of the similarly high barrier, 7 kJ/mol, near the exit of the pore.

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Zhu, Ting, Ju Li, and Sidney Yip. "Atomistic characterization of three-dimensional lattice trapping barriers to brittle fracture." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 462, no. 2070 (February 21, 2006): 1741–61. http://dx.doi.org/10.1098/rspa.2005.1567.

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We present a detailed account of an atomistic study of three-dimensional lattice trapping barriers to brittle fracture in Si. By means of a prototypical interatomic potential model, we map out the molecular details of the evolution of atomically sharp cracks in the (111) cleavage plane with straight crack fronts along the and directions, respectively. The thermally activated processes of bond rupturing along the crack front are quantitatively characterized using a reaction pathway sampling scheme. The calculated minimum energy paths reveal a mechanism of kink-pair formation and migration in facilitating the crack front advancement. We show that the physical origin of directional anisotropy in cleavage crack propagation can be attributed to a difference in the kink-pair formation energy for different crack orientations. The effects of interatomic potentials are delineated by comparing the Stillinger–Weber model with an environment-dependent model.

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Morsy, Omar, Farzad Hourfar, Qinqin Zhu, Ali Almansoori, and Ali Elkamel. "A Superstructure Mixed-Integer Nonlinear Programming Optimization for the Optimal Processing Pathway Selection of Sludge-to-Energy Technologies." Sustainability 15, no. 5 (February 22, 2023): 4023. http://dx.doi.org/10.3390/su15054023.

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The perception of sewage sludge has increasingly changed from being a waste, which is a burden to the environment and society, to a useful resource of materials and renewable energy. There are several available technologies at different stages of maturity that aim to convert sludge to energy in the form of electricity and/or fuels. In this paper, a decision-making support tool is proposed to help in choosing the optimal pathway for the sludge-to-energy conversion from a techno-economic perspective. The conversion technologies under study are: (1) anaerobic digestion, (2) pyrolysis, (3) gasification, (4) incineration, (5) supercritical water oxidation, (6) supercritical water gasification, as well as the corresponding dewatering and drying methods for each technology. Different synergies between the available technologies are compared by the formulation of a superstructure optimization problem expressed in a mixed-integer non-linear program (MINLP) model. The applicability of the proposed model is explored via a case study for a hypothetical sludge treatment plant with a capacity of 100 tons of dry solids (tDS) per day. The model is solved via the BARON solver using GAMS software within a reasonable processing time. According to the obtained results, the fast pyrolysis technology, coupled with filter press dewatering and thermal drying as pre-treatment steps, show the most promising outcomes with the minimum treatment cost of USD 180/tDS. Fast pyrolysis converts the sludge to bio-oil, which can be used as an alternative fuel after further refining, and biochar, which can be used for soil amendment or adsorption purposes. The model parameters are subject to uncertainty that is addressed in the sensitivity analysis section of this paper. Moreover, the pyrolysis pathway shows a high degree of robustness in most of the sensitivity analysis scenarios. Meanwhile, anaerobic digestion coupled with fast pyrolysis demonstrates the best energy recovery performance upon increasing electricity prices.

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Khrenova, Maria G., Egor S. Bulavko, Fedor D. Mulashkin, and Alexander V. Nemukhin. "Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials." Molecules 26, no. 13 (June 30, 2021): 3998. http://dx.doi.org/10.3390/molecules26133998.

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We report the results of calculations of the Gibbs energy profiles of the guanosine triphosphate (GTP) hydrolysis by the Arl3-RP2 protein complex using molecular dynamics (MD) simulations with ab initio type QM/MM potentials. The chemical reaction of GTP hydrolysis to guanosine diphosphate (GDP) and inorganic phosphate (Pi) is catalyzed by GTPases, the enzymes, which are responsible for signal transduction in live cells. A small GTPase Arl3, catalyzing the GTP → GDP reaction in complex with the activating protein RP2, constitute an essential part of the human vision cycle. To simulate the reaction mechanism, a model system is constructed by motifs of the crystal structure of the Arl3-RP2 complexed with a substrate analog. After selection of reaction coordinates, energy profiles for elementary steps along the reaction pathway GTP + H2O → GDP + Pi are computed using the umbrella sampling and umbrella integration procedures. QM/MM MD calculations are carried out, interfacing the molecular dynamics program NAMD and the quantum chemistry program TeraChem. Ab initio type QM(DFT)/MM potentials are computed with atom-centered basis sets 6-31G** and two hybrid functionals (PBE0-D3 and ωB97x-D3) of the density functional theory, describing a large QM subsystem. Results of these simulations of the reaction mechanism are compared to those obtained with QM/MM calculations on the potential energy surface using a similar description of the QM part. We find that both approaches, QM/MM and QM/MM MD, support the mechanism of GTP hydrolysis by GTPases, according to which the catalytic glutamine side chain (Gln71, in this system) actively participates in the reaction. Both approaches distinguish two parts of the reaction: the cleavage of the phosphorus-oxygen bond in GTP coupled with the formation of Pi, and the enzyme regeneration. Newly performed QM/MM MD simulations confirmed the profile predicted in the QM/MM minimum energy calculations, called here the pathway-I, and corrected its relief at the first elementary step from the enzyme–substrate complex. The QM/MM MD simulations also revealed another mechanism at the part of enzyme regeneration leading to pathway-II. Pathway-II is more consistent with the experimental kinetic data of the wild-type complex Arl3-RP2, whereas pathway-I explains the role of the mutation Glu138Gly in RP2 slowing down the hydrolysis rate.

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Ugarte, Ricardo, Guillermo Salgado, and Luis Basáez. "A theoretical study of the nitration of eugenol with the nitronium ion." Collection of Czechoslovak Chemical Communications 76, no. 12 (2011): 1529–48. http://dx.doi.org/10.1135/cccc2011156.

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The nitration of eugenol was investigated by using density functional theory (DFT) calculations. Potential energy surface and molecular electrostatic potential of eugenol was constructed in order to find, respectively, the minimum energy conformers and the possible sites for electrophilic attack. Stationary points were located and characterized at the B3LYP/6-311++G(2d,2p) level of theory. A strongly bound π-complex was found, in which the distance between the nitrogen atom of the NO2 moiety and the C1 carbon atom of the aromatic ring is 2.15 Å in the gas phase and 2.06 Å in dichloromethane. The most favorable σ-complex or Wheland intermediate is the result from the interaction between the nitrogen and the C6 ring carbon atom. The transition state that connects both complexes is more resembling the σ-complex. The nitronium ion exothermically reacts with eugenol to give the π-complex without an energy barrier. The next stage of the reaction pathway, π-complex → σ-complex, is endothermic and involves a Gibbs energy of activation of 7.9–8.0 kcal mol–1 (gas phase) and 8.3–8.9 kcal mol–1 (CH2Cl2).

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Kathan, Michael, Stefano Crespi, Niklas O. Thiel, Daniel L. Stares, Denis Morsa, John de Boer, Gianni Pacella, et al. "A light-fuelled nanoratchet shifts a coupled chemical equilibrium." Nature Nanotechnology 17, no. 2 (December 16, 2021): 159–65. http://dx.doi.org/10.1038/s41565-021-01021-z.

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AbstractBiological molecular machines enable chemical transformations, assembly, replication and motility, but most distinctively drive chemical systems out of-equilibrium to sustain life1,2. In such processes, nanometre-sized machines produce molecular energy carriers by driving endergonic equilibrium reactions. However, transforming the work performed by artificial nanomachines3–5 into chemical energy remains highly challenging. Here, we report a light-fuelled small-molecule ratchet capable of driving a coupled chemical equilibrium energetically uphill. By bridging two imine6–9 macrocycles with a molecular motor10,11, the machine forms crossings and consequently adopts several distinct topologies by either a thermal (temporary bond-dissociation) or photochemical (unidirectional rotation) pathway. While the former will relax the machine towards the global energetic minimum, the latter increases the number of crossings in the system above the equilibrium value. Our approach provides a blueprint for coupling continuous mechanical motion performed by a molecular machine with a chemical transformation to reach an out-of-equilibrium state.

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Bageshwar, Umesh K., and Siegfried M. Musser. "Two electrical potential–dependent steps are required for transport by the Escherichia coli Tat machinery." Journal of Cell Biology 179, no. 1 (October 1, 2007): 87–99. http://dx.doi.org/10.1083/jcb.200702082.

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The twin-arginine translocation (Tat) pathway in Escherichia coli transports fully folded and assembled proteins across the energy-transducing periplasmic membrane. In chloroplasts, Tat transport requires energy input only from the proton motive force. To elucidate the mechanism and energetics of bacterial Tat protein transport, we developed an efficient in vitro transport assay using TatABC-enriched inverted membrane vesicles and the physiological precursor pre-SufI. We report transport efficiencies of 60–80% for nanomolar pre-SufI concentrations. Dissipation of the pH gradient does not reduce pre-SufI transport efficiency. Instead, pre-SufI transport requires at least two electrical potential (Δψ)–dependent steps that differ in both the duration and minimum magnitude of the required Δψ. The data are consistent with a model in which a substantial Δψ of short duration is required for an early transport step, and in which a small Δψ of long duration is necessary to drive a later transport step.

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Khanal, Pukar, B. M. Patil, Jagdish Chand, and Yasmin Naaz. "Anthraquinone Derivatives as an Immune Booster and their Therapeutic Option Against COVID-19." Natural Products and Bioprospecting 10, no. 5 (August 8, 2020): 325–35. http://dx.doi.org/10.1007/s13659-020-00260-2.

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Abstract Anthraquinone derivatives are identified for their immune-boosting, anti-inflammatory, and anti-viral efficacy. Hence, the present study aimed to investigate the reported anthraquinone derivatives as immune booster molecules in COVID-19 infection and evaluate their binding affinity with three reported targets of novel coronavirus i.e. 3C-like protease, papain-like protease, and spike protein. The reported anthraquinone derivatives were retrieved from an open-source database and filtered based on a positive druglikeness score. Compounds with positive druglikeness scores were predicted for their targets using DIGEP-Pred and the interaction among modulated proteins was evaluated using STRING. Further, the associated pathways were recorded concerning the Kyoto Encyclopedia of Genes and Genomes pathway database. Finally, the docking was performed using autodock4 to identify the binding efficacy of anthraquinone derivatives with 3C-like protease, papain-like protease, and spike protein. After docking the pose of ligand scoring minimum binding energy was chosen to visualize the ligand–protein interaction. Among 101 bioactives, 36 scored positive druglikeness score and regulated multiple pathways concerned with immune modulation and (non-) infectious diseases. Similarly, docking study revealed torososide B to possess the highest binding affinity with papain-like protease and 3C-like protease and 1,3,6-trihydroxy-2-methyl-9,10-anthraquinone-3-O-(6′-O-acetyl)-β-d-xylopyranosyl-(1 → 2)-β-d-glucopyranoside with spike protein. Graphic Abstract

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Hussain, Zakir, Deepa Meghavathu, and Rakesh Kumar. "Glimpses Of Dynamic Biodiesel Product Pricing Model." International Journal of Engineering & Technology 7, no. 4.5 (September 22, 2018): 224. http://dx.doi.org/10.14419/ijet.v7i4.5.20051.

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Entrepreneurship development, energy crisis, rising fossil fuel prices, increasing greenhouse gas emission and waste management are the key issues which concern the government to tackle them sustainably. The advent of biodiesel as a fuel paves the pathway to handle these issues and together it creates an opportunity to develop a small/medium to large-scale biodiesel production units. Current research is mainly focused on creating the roadmap to solve the feedstock scarcity issue faced by Indian biodiesel industries through the field survey. It also presents a robust model framework to fix the minimum selling price of biodiesel through energy input-output and cost input-out analysis in producing a unit volume of biodiesel. The results show that the surveyed area may have the potential to supply on an average of 129 liters/day waste vegetable oil. Energy analysis shows that the highest share of energy 71.84% was from waste vegetable oil followed by 25.99% corresponds to alcohol. Others are being at 0.85% due to the catalyst, 0.44% due to electricity, 0.68% due to machinery and 0.2% due to human labor. Cost analysis shows that the highest share of cost 52.13% was due to alcohol followed by 39.34% due to waste cooking oil.

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Kumari, Sweta, Sri Sadgun Reddy Pulagam, and Amlan Dutta. "Nucleation of Twinning Dislocation Loop in Pt: A Computational Approach." International Journal of Innovative Research in Physics 3, no. 1 (October 4, 2021): 11–18. http://dx.doi.org/10.15864/ijiip.3102.

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Twinning plays a critical part in the plastic deformation of the materials and the strengthening mechanisms and is hence considered as one of the most prevalent deformation mechanisms in metals. Because to the high stacking fault energy of the fcc metals like Al, Pd, and Pt, the extended dislocations are believed to be energetically favored over isolated partials, thereby rendering deformation twinning unfeasible. Nevertheless, some recent experimental researches have confirmed a potential deformation twinning pathway in nanocrystalline platinum. This alternate-shear mechanism has a much lower energy barrier than the usual layer-by-layer twinning. We utilize computations involving atomistic calculations and continuum modeling in this study to examine the genesis of deformation twins in Pt. Atomistic simulations provides the generalized planer fault energy using an EAM (embedded-atom-model) potential. Moreover, a potential energy-based method, namely; a nudged-elastic band (chain of states) has been used to compute the activation energy barrier for the nucleation of the twinning dislocation loop in the alternate-shear model. The critical stress needed for the nucleation of the twinning dislocation loop in platinum is estimated using some of the parameters acquired from atomistic calculations and using them as fitting parameters in the continuum model. The minimum-energy path between the two end states can be identified using this methodology. Through the unusual alternate-shear approach, the results provide a rudimentary but essential dislocationbased perspective of the occurrence of deformation twins in fcc metals.

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Choi, Yong Hyun, and Joonsik Hwang. "Review on Plasma-Assisted Ignition Systems for Internal Combustion Engine Application." Energies 16, no. 4 (February 6, 2023): 1604. http://dx.doi.org/10.3390/en16041604.

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Due to the depletion of conventional petroleum-based fuels and increasing environmental concerns, industries have been developing new combustion technologies with acceptable cost ranges and minimum system modifications for consumers. Among many approaches, the utilization of plasma ignition systems is considered as a promising pathway to achieve greener transportation while maintaining conventional internal combustion engine systems. Plasma contains highly reactive radicals, and those have a great potential of enhancing chemical reactions that are beneficial for reducing carbon emissions. The primary objective of this paper is to provide an overview of currently available plasma-assisted combustion systems including recent achievements in research and development, and technical challenges for successfully implementing a new ignition system. This review will introduce various plasma-assisted combustion approaches from worldwide projects, covering non-thermal and thermal plasma systems in internal combustion engines.

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Yoshida, Norio. "A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method." Chemical Physics Letters 699 (May 2018): 22–27. http://dx.doi.org/10.1016/j.cplett.2018.03.034.

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Lemuth, K., T. Hardiman, S. Winter, D. Pfeiffer, M. A. Keller, S. Lange, M. Reuss, R. D. Schmid, and M. Siemann-Herzberg. "Global Transcription and Metabolic Flux Analysis of Escherichia coli in Glucose-Limited Fed-Batch Cultivations." Applied and Environmental Microbiology 74, no. 22 (September 19, 2008): 7002–15. http://dx.doi.org/10.1128/aem.01327-08.

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ABSTRACT A time series of whole-genome transcription profiling of Escherichia coli K-12 W3110 was performed during a carbon-limited fed-batch process. The application of a constant feed rate led to the identification of a dynamic sequence of diverse carbon limitation responses (e.g., the hunger response) and at the same time provided a global view of how cellular and extracellular resources are used: the synthesis of high-affinity transporters guarantees maximal glucose influx, thereby preserving the phosphoenolpyruvate pool, and energy-dependent chemotaxis is reduced in order to provide a more economic “work mode.” σS-mediated stress and starvation responses were both found to be of only minor relevance. Thus, the experimental setup provided access to the hunger response and enabled the differentiation of the hunger response from the general starvation response. Our previous topological model of the global regulation of the E. coli central carbon metabolism through the crp, cra, and relA/spoT modulons is supported by correlating transcript levels and metabolic fluxes and can now be extended. The substrate is extensively oxidized in the tricarboxylic acid (TCA) cycle to enhance energy generation. However, the general rate of oxidative decarboxylation within the pentose phosphate pathway and the TCA cycle is restricted to a minimum. Fine regulation of the carbon flux through these pathways supplies sufficient precursors for biosyntheses. The pools of at least three precursors are probably regulated through activation of the (phosphoenolpyruvate-)glyoxylate shunt. The present work shows that detailed understanding of the genetic regulation of bacterial metabolism provides useful insights for manipulating the carbon flux in technical production processes.

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Berry, C. A. "Characteristics of water diffusion in the rabbit proximal convoluted tubule." American Journal of Physiology-Renal Physiology 249, no. 5 (November 1, 1985): F729—F738. http://dx.doi.org/10.1152/ajprenal.1985.249.5.f729.

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Water diffusion in the in vitro microperfused rabbit proximal convoluted tubule was measured to assess the transepithelial pathway for water movement and the physical characteristics of the water permeation pathway. The measured diffusive water permeability (PDW(MEASURED] was high, 5 X 10(-3) cm/s, suggesting a transcellular transport route. Simultaneously measured n-butanol permeability (PDNB(MEASURED], an index of the cytoplasmic resistance to water diffusion, was 3.6 X 10(-3) cm/s. PDW(MEASURED], PDNB(MEASURED) and the free solution diffusion coefficients for water and n-butanol were used to derive a minimum membrane PDW (PDW(MEMBRANE] of 12.5 X 10(-3) cm/s. These data suggest that at least 60% of the transepithelial resistance to water diffusion resides in the cell cytoplasm. Measurement of the temperature dependence of PDW(MEASURED) and PDNB(MEASURED) gave an apparent activation energy of PDW(MEMBRANE) that was constant between 20 and 40 degrees C at about 4.3 kcal/mol. The organic mercurial sulfhydryl reagent p-chloromercuribenzene sulfonate, which has been shown to reduce diffusive water permeability in the red cell membrane by 50%, reduced PDW(MEMBRANE) by 54% without affecting PDNB(MEASURED). These last two independent lines of evidence are consistent with water diffusion through small, aqueous, protein-bounded channels.

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Boyer, David R., Binsen Li, Chuanqi Sun, Weijia Fan, Kang Zhou, Michael P. Hughes, Michael R. Sawaya, Lin Jiang, and David S. Eisenberg. "The α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure." Proceedings of the National Academy of Sciences 117, no. 7 (February 3, 2020): 3592–602. http://dx.doi.org/10.1073/pnas.1917914117.

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Aggregation of α-synuclein is a defining molecular feature of Parkinson’s disease, Lewy body dementia, and multiple systems atrophy. Hereditary mutations in α-synuclein are linked to both Parkinson’s disease and Lewy body dementia; in particular, patients bearing the E46K disease mutation manifest a clinical picture of parkinsonism and Lewy body dementia, and E46K creates more pathogenic fibrils in vitro. Understanding the effect of these hereditary mutations on α-synuclein fibril structure is fundamental to α-synuclein biology. We therefore determined the cryo-electron microscopy (cryo-EM) structure of α-synuclein fibrils containing the hereditary E46K mutation. The 2.5-Å structure reveals a symmetric double protofilament in which the molecules adopt a vastly rearranged, lower energy fold compared to wild-type fibrils. We propose that the E46K misfolding pathway avoids electrostatic repulsion between K46 and K80, a residue pair which form the E46-K80 salt bridge in the wild-type fibril structure. We hypothesize that, under our conditions, the wild-type fold does not reach this deeper energy well of the E46K fold because the E46-K80 salt bridge diverts α-synuclein into a kinetic trap—a shallower, more accessible energy minimum. The E46K mutation apparently unlocks a more stable and pathogenic fibril structure.

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Journal articles on the topic 'Minimum Energy Pathway'

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