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Journal articles on the topic 'Minimum Energy Pathway'

Author: Grafiati

Published: 14 March 2023

Last updated: 31 July 2025

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1

Philippe, T., and D. Blavette. "Minimum free-energy pathway of nucleation." Journal of Chemical Physics 135, no. 13 (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 (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 Gaus

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Borodin, Dmitriy, Igor Rahinov, Pranav R. Shirhatti, et al. "Following the microscopic pathway to adsorption through chemisorption and physisorption wells." Science 369, no. 6510 (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-ph

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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 (2011): 31–40. http://dx.doi.org/10.1140/epjb/e2011-10629-9.

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5

Bouallagui, A., A. Zanchet, M. Mogren Al Mogren, L. Bañares, and A. García-Vela. "A High-level Ab Initio Study of the Destruction of Methanimine under UV Radiation." Astrophysical Journal 956, no. 1 (2023): 22. http://dx.doi.org/10.3847/1538-4357/acf311.

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Abstract The photodecomposition of methanimine (CH2NH) in the interstellar medium through several possible pathways is investigated by means of high-level multireference configuration interaction ab initio calculations. Among these pathways are photodissociation pathways involving hydrogen-atom elimination from both the CH2 and NH groups, and fragmentation into CH2 and NH. Potential-energy curves for the ground and several excited electronic states, as well as nonadiabatic couplings between them, are calculated. Possible dissociation mechanisms are discussed for the different pathways. It is f

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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 (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. Usi

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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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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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Singh, Baltej, Mayanak Kumar Gupta, Ranjan Mittal та ін. "Superionic conduction in β-eucryptite: inelastic neutron scattering and computational studies". Physical Chemistry Chemical Physics 19, № 23 (2017): 15512–20. http://dx.doi.org/10.1039/c7cp01490b.

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Monferrer, Ezequiel, Isaac Vieco-Martí, Amparo López-Carrasco, et al. "Metabolic Classification and Intervention Opportunities for Tumor Energy Dysfunction." Metabolites 11, no. 5 (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 inv

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11

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 (2012): 107101. http://dx.doi.org/10.1063/1.3692688.

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12

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 (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

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Lu, Yanxia, Qing Peng, and Chenguang Liu. "Ab Initio Investigation of Helium Mobility in La2Zr2O7 Pyrochlore." Crystals 11, no. 6 (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 bar

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14

Zhu, Ting, Ju Li, and Sidney Yip. "Nanomechanics of Crack Front Mobility." Journal of Applied Mechanics 72, no. 6 (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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15

R, Jerlinkasmir, and Veninstine Vivik J. "Analyzing Pathway Energy And Time Complexity In Flower Families Through Vertex-Disjoint Paths." Journal of Combinatorial Mathematics and Combinatorial Computing 123, no. 1 (2024): 197–219. https://doi.org/10.61091/jcmcc123-14.

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This research delves into the pathway energy framework for flower families, a class of simple connected graphs, whose path matrix p is constructed such that each entry pij quantifies the maximum number of vertex-disjoint paths. By analyzing the characteristic values of this matrix, we establish the pathway energy bounds specific to these flower graph families. Additionally, a comprehensive algorithm is developed to evaluate the time complexity across different flower family configurations, utilizing numerous trials to capture their average, maximum, and minimum computational behaviors. This an

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16

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 (2012): 14178–82. http://dx.doi.org/10.1021/jp310008z.

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17

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 (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. T

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18

Potkina, M. N., and I. S. Lobanov. "Optimality of linear vacancy defect for skyrmion nucleation." Nanosystems: Physics, Chemistry, Mathematics 16, no. 3 (2025): 317–24. https://doi.org/10.17586/2220-8054-2025-16-3-317-324.

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Magnetic skyrmions offer a pathway to ultra-dense, low-power memory, but writing them efficiently remains a challenge. Using atomistic spin simulations and minimum energy path calculations in a PdFe/Ir(111) film, we show that deliberately placing linear chains of four atomic vacancies cuts the skyrmion nucleation barrier nearly in half-down to 44.7 meV at 3.75 T-compared to 85 meV in a pristine track. Linear defects excel because they remove high-energy core regions during skyrmion creation while minimally disturbing its outer negative energy halo during depinning. This geometry-driven effect

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19

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 (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 dockin

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20

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 (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 thi

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21

Digiesi, Salvatore, Giovanni Mummolo, and Micaela Vitti. "Minimum Emissions Configuration of a Green Energy–Steel System: An Analytical Model." Energies 15, no. 9 (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 po

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22

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 competiti

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23

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 (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 intercellu

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24

Cruzeiro, Leonor. "The VES KM: a pathway for protein folding in vivo." Pure and Applied Chemistry 92, no. 1 (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 it

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25

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 (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 th

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26

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 (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 b

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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 (2010): 1195–203. http://dx.doi.org/10.1021/jp106523b.

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28

Kanematsu, Yusuke, Hiroko X. Kondo, and Yu Takano. "Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model." International Journal of Molecular Sciences 24, no. 24 (2023): 17172. http://dx.doi.org/10.3390/ijms242417172.

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P450nor is a heme-containing enzyme that catalyzes the conversion of nitric oxide (NO) to nitrous oxide (N2O). Its catalytic mechanism has attracted attention in chemistry, biology, and environmental engineering. The catalytic cycle of P450nor is proposed to consist of three major steps. The reaction mechanism for the last step, N2O generation, remains unknown. In this study, the reaction pathway of the N2O generation from the intermediate I was explored with the B3LYP calculations using an active center model after the examination of the validity of the model. In the validation, we compared t

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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 (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)

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30

Li, Zhenxing, Yan-lin Fu, Zijie Luo, et al. "Roaming in highly excited states: The central atom elimination of triatomic molecule decomposition." Science 383, no. 6684 (2024): 746–50. http://dx.doi.org/10.1126/science.adn3357.

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Chemical reactions are generally assumed to proceed from reactants to products along the minimum energy path (MEP). However, straying from the MEP—roaming—has been recognized as an unconventional reaction mechanism and found to occur in both the ground and first excited states. Its existence in highly excited states is however not yet established. We report a dissociation channel to produce electronically excited fragments, S( 1 D)+O 2 (a 1 Δ g ), from SO 2 photodissociation in highly excited states. The results revealed two dissociation pathways: One proceeds through the MEP to produce vibrat

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31

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 (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 investig

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32

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 (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 cat

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Sun, Qiao, Sufan Wang, Hong Zhang, et al. "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 prot

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34

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 (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

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35

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 (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 bun

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36

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 certainl

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37

Fujimoto, Kazushi, Motohiro Fukai, Ryo Urano, et al. "Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation." Pure and Applied Chemistry 92, no. 10 (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 (

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38

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 (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 synt

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39

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 (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 h

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40

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 (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

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He, Chenchen, Jieru Hu, and Meng Li. "Mechanism of Fuzheng Jiedu Huayu Decoction in the Treatment of Sepsis based on Network Pharmacology and Molecular Docking." Journal of Contemporary Medical Practice 7, no. 2 (2025): 82–88. https://doi.org/10.53469/jcmp.2025.07(02).16.

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Objective: Using network pharmacology and molecular docking techniques, we explored the active ingredients in Fuzheng Jiedu Huayu Decoction (FJHD) and predicted its potential mechanisms of action in treating sepsis, providing a theoretical basis for the clinical application of FJHD. Methods: Using the TCMSP platform to screen for active ingredients and their targets in FJHD; obtaining sepsis-related target genes using the GeneCards, OMIM, and TTD databases; intersecting drug targets with disease-related targets using the Venny 2.1.0 platform; constructing drug-active ingredient-target networks

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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 (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 fa

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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 (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 phosphorylatio

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Ali, Babkir, and Ahmed Gamil. "Scenario-Based Optimization towards Sustainable Power Generation in Sudan." Sustainability 15, no. 20 (2023): 14954. http://dx.doi.org/10.3390/su152014954.

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Sudan faces an electricity supply shortage despite its abundant natural resources. This paper aims to manage these resources for sustainable power generation to meet Sudan’s electricity demand. The sustainability assessment integrates quantitative analysis of power generation’s impacts on water, land, and greenhouse gas (GHG) emissions, in addition to the levelized cost of electricity (LCOE). Cost-effective, resource- and GHG emission-effective, and GHG-stringent scenarios are executed in this study to investigate the impact of different constraints on the sustainability of power generation in

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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 (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 reac

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Zhang, Yange, Peiyun Ji, Xiangyu Xiao, et al. "Network pharmacology, molecular docking, and molecular dynamics simulations shed light on the mechanism behind Gynostemma pentaphyllum’s efficacy against osteosarcoma." Medicine 103, no. 35 (2024): e39454. http://dx.doi.org/10.1097/md.0000000000039454.

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Osteosarcoma (OS) is the most common type of malignant bone tumor, that poses a serious threat to the lives and health of children and adolescents. Traditional Chinese medicines (TCM) have gained attention for treating OS because of their potent anti-cancer effects and fewer side effects. It is commonly understood that Gynostemma pentaphyllum (Thunb.) Makino (GP) exhibits inhibitory effects on most tumors. However, the knowledge of the systematic mechanisms involved is limited. In this study, the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was searc

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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. T

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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 (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) gasific

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Kathan, Michael, Stefano Crespi, Niklas O. Thiel, et al. "A light-fuelled nanoratchet shifts a coupled chemical equilibrium." Nature Nanotechnology 17, no. 2 (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 w

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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 (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 reduc

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