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Journal articles on the topic 'Molecular Energy - Dynamical Correlation'

Author: Grafiati

Published: 7 September 2023

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1

Feng, Hai-Ran, Xiang-Jia Meng, Peng Li, and Yu-Jun Zheng. "Dynamical correlation between quantum entanglement and intramolecular energy in molecular vibrations: An algebraic approach." Chinese Physics B 23, no. 7 (2014): 073301. http://dx.doi.org/10.1088/1674-1056/23/7/073301.

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2

HWA, RUDOLPH C. "GEOMETRICAL AND DYNAMICAL MULTIPLICITY FLUCTUATIONS IN HIGH-ENERGY NUCLEAR COLLISIONS." International Journal of Modern Physics A 04, no. 02 (1989): 481–92. http://dx.doi.org/10.1142/s0217751x89000248.

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General properties of multiplicity fluctuation in high-energy nuclear collisions are considered. Quantities that can directly be related to the geometrical and dynamical sources of the fluctuation are identified. Formalism for treating impact-parameter selection is discussed. The connection with correlation is described. Recent data indicate the absence of any significant collective behavior in the current experiments at the SPS. The observable that can reveal the onset of such behavior is suggested.

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3

MAKRI, NANCY, AKIRA NAKAYAMA, and NICHOLAS J. WRIGHT. "FORWARD-BACKWARD SEMICLASSICAL SIMULATION OF DYNAMICAL PROCESSES IN LIQUIDS." Journal of Theoretical and Computational Chemistry 03, no. 03 (2004): 391–417. http://dx.doi.org/10.1142/s0219633604001112.

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Forward-backward semiclassical dynamics (FBSD) provides a practical methodology for including quantum mechanical effects in classical trajectory simulations of polyatomic systems. FBSD expressions for time-dependent expectation values or correlation functions take the form of phase space integrals with respect to trajectory initial conditions, weighted by the coherent state transform of a corrected density operator. Quantization through a discretized path integral representation of the Boltzmann operator ensures a proper treatment of zero point energy effects and of imaginary components in fin

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4

PAPA, M., and G. GIULIANI. "DYNAMICAL CORRELATIONS AND THE SYMMETRY INTERACTION." International Journal of Modern Physics E 17, no. 10 (2008): 2320–25. http://dx.doi.org/10.1142/s0218301308011549.

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It is shown how many-body correlations involving the symmetry potential naturally arise in the molecular dynamics CoMD-II model. The effect of these correlations on the collision dynamics at the Fermi energies is briefly discussed. The comparison with predictions based on the density functional as obtained through EOS static calculations is also discussed.

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5

Yuan, Qiang, and Xi-Wen Hou. "Entropy, energy, and entanglement of localized states in bent triatomic molecules." International Journal of Modern Physics B 31, no. 12 (2017): 1750088. http://dx.doi.org/10.1142/s0217979217500886.

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The dynamics of quantum entropy, energy, and entanglement is studied for various initial states in an important spectroscopic Hamiltonian of bent triatomic molecules H2O, D2O, and H2S. The total quantum correlation is quantified in terms of the mutual information and the entanglement by the concurrence borrowed from the theory of quantum information. The Pauli entropy and the intramolecular energy usually used in the theory of molecules are calculated to establish a possible relationship between both theories. Sections of two quantities among these four quantities are introduced to visualize s

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Finn, Molly K., Remy Indebetouw, Kelsey E. Johnson, et al. "Structural and Dynamical Analysis of the Quiescent Molecular Ridge in the Large Magellanic Cloud." Astronomical Journal 164, no. 2 (2022): 64. http://dx.doi.org/10.3847/1538-3881/ac7aa1.

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Abstract We present a comparison of low-J 13CO and CS observations of four different regions in the LMC—the quiescent Molecular Ridge, 30 Doradus, N159, and N113, all at a resolution of ∼3 pc. The regions 30 Dor, N159, and N113 are actively forming massive stars, while the Molecular Ridge is forming almost no massive stars, despite its large reservoir of molecular gas and proximity to N159 and 30 Dor. We segment the emission from each region into hierarchical structures using dendrograms and analyze the sizes, masses, and line widths of these structures. We find that the Ridge has significantl

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7

Bonačič-Koutecký, Vlasta, Detlef Reichardt, Jiří Pittner, Piercarlo Fantucci, and Jaroslav Koutecký. "Ab initio Molecular Dynamics for Determination of Structures of Alkali Metal Clusters and Their Temperatures Behavior; An Example of Li9+." Collection of Czechoslovak Chemical Communications 63, no. 9 (1998): 1431–46. http://dx.doi.org/10.1135/cccc19981431.

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It will be shown that an ab initio molecular dynamics procedure based on gradient corrected density functionals for exchange and correlation and using a Gaussian atomic basis (AIMD-GDF) implemented for parallel processing represents a suitable tool for detailed and accurate investigation of structural and dynamical properties of small systems. Gradients of the Born-Oppenheimer ground state energy, obtained by iterative solution of the Kohn-Sham equations, are used to calculate the forces acting on atoms at each instantaneous configuration along trajectories generated by solving classical equat

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8

Kiselev, S. M. "Azimuthal multiparticle correlations in high-energy heavy-ion collisions in the molecular-dynamical model." Physics Letters B 216, no. 3-4 (1989): 262–66. http://dx.doi.org/10.1016/0370-2693(89)91112-x.

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9

Comes, F. J. "Vector Correlations in Molecular Photofragmentations." Laser Chemistry 11, no. 3-4 (1991): 151–56. http://dx.doi.org/10.1155/lc.11.151.

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Photofragmentation spectroscopy—the study of “half collisions” with polarized light of subdoppler line width—opens a window to look into the structure of molecules. The energy partitioning among the particular degrees of freedom of the products of the fragmentation reaction is described by the scalar properties, the direction and magnitude of a particular type of motion is described by the vector properties. The measurement of the scalar and vector properties allows a pictorial view of the intermediate state. The forces which make the fragments fly apart or rotate and vibrate can be “seen” fro

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10

ZHANG, JINGBO, QICHUN FENG, LEI HUO, and WEINING ZHANG. "TWO-PARTICLE CORRELATION IN HEAVY-ION COLLISIONS AT CSR ENERGY." International Journal of Modern Physics E 16, no. 07n08 (2007): 2200–2204. http://dx.doi.org/10.1142/s0218301307007684.

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The predictions of the two-particle correlation by using the relativistic quantum molecular dynamics model are presented for the heavy-ion reactions at HIRFL-CSR energy. The two-proton correlation function with the final state interaction is calculated with the Lednicky code for the U + U collisions at beam energy 520 A MeV. Applying the imaging technique, the relationship between the freeze-out spatial distributions and the results of correlation femtoscopy is investigated. We find that one can reliably reconstruct the source functions from the two-particle correlation functions with ignoring

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11

Inoue, Hajime. "Wandering of the central black hole in a galactic nucleus and correlation of the black hole mass with the bulge mass." Publications of the Astronomical Society of Japan 73, no. 2 (2021): 431–38. http://dx.doi.org/10.1093/pasj/psab009.

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Abstract We investigate a mechanism for a super-massive black hole at the center of a galaxy to wander in the nucleus region. A situation is supposed in which the central black hole tends to move by the gravitational attractions from the nearby molecular clouds in a nuclear bulge but is braked via the dynamical frictions from the ambient stars there. We estimate the approximate kinetic energy of the black hole in an equilibrium between the energy gain rate through the gravitational attractions and the energy loss rate through the dynamical frictions in a nuclear bulge composed of a nuclear ste

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12

Jeffreson, Sarah M. R., J. M. Diederik Kruijssen, Benjamin W. Keller, Mélanie Chevance, and Simon C. O. Glover. "The role of galactic dynamics in shaping the physical properties of giant molecular clouds in Milky Way-like galaxies." Monthly Notices of the Royal Astronomical Society 498, no. 1 (2020): 385–429. http://dx.doi.org/10.1093/mnras/staa2127.

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ABSTRACT We examine the role of the large-scale galactic-dynamical environment in setting the properties of giant molecular clouds in Milky Way-like galaxies. We perform three high-resolution simulations of Milky Way-like discs with the moving-mesh hydrodynamics code arepo, yielding a statistical sample of ${\sim}80\, 000$ giant molecular clouds and ${\sim}55\, 000$ H i clouds. We account for the self-gravity of the gas, momentum, and thermal energy injection from supernovae and H ii regions, mass injection from stellar winds, and the non-equilibrium chemistry of hydrogen, carbon, and oxygen.

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Huang, Kaisheng, Yi Liu, Shuixiu Wen та ін. "Binding Mechanism of CD47 with SIRPα Variants and Its Antibody: Elucidated by Molecular Dynamics Simulations". Molecules 28, № 12 (2023): 4610. http://dx.doi.org/10.3390/molecules28124610.

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The intricate complex system of the differentiation 47 (CD47) and the signal-regulatory protein alpha (SIRPα) cluster is a crucial target for cancer immunotherapy. Although the conformational state of the CD47-SIRPα complex has been revealed through crystallographic studies, further characterization is needed to fully understand the binding mechanism and to identify the hot spot residues involved. In this study, molecular dynamics (MD) simulations were carried out for the complexes of CD47 with two SIRPα variants (SIRPαv1, SIRPαv2) and the commercially available anti-CD47 monoclonal antibody (

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14

Alba-Arroyo, J. E., S. F. Caballero-Benitez, and R. Jáuregui. "Rotational Dynamics Induced by Low-Energy Binary Collisions of Quantum Droplets." Photonics 10, no. 7 (2023): 823. http://dx.doi.org/10.3390/photonics10070823.

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A theoretical analysis of the rotational dynamics induced by off-axis binary collisions of quantum droplets constituted by ultracold atoms is reported. We focus on quantum droplets formed by degenerate dilute Bose gases made from binary mixtures of alkaline atoms under feasible experimental conditions. The stability of the ground state is known to be longer for the chosen heteronuclear gases than for the homonuclear ones. In both cases, we find that the dynamics seem to privilege high similarity of the density of each atomic species. However, the evolution of the phase of the corresponding ord

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15

Kondo, Toru, Jesse B. Gordon, Alberta Pinnola, Luca Dall’Osto, Roberto Bassi, and Gabriela S. Schlau-Cohen. "Microsecond and millisecond dynamics in the photosynthetic protein LHCSR1 observed by single-molecule correlation spectroscopy." Proceedings of the National Academy of Sciences 116, no. 23 (2019): 11247–52. http://dx.doi.org/10.1073/pnas.1821207116.

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Biological systems are subjected to continuous environmental fluctuations, and therefore, flexibility in the structure and function of their protein building blocks is essential for survival. Protein dynamics are often local conformational changes, which allows multiple dynamical processes to occur simultaneously and rapidly in individual proteins. Experiments often average over these dynamics and their multiplicity, preventing identification of the molecular origin and impact on biological function. Green plants survive under high light by quenching excess energy, and Light-Harvesting Complex

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16

Yang, C. B., and X. Cai. "Quantitative Measure of Dynamical Fluctuations in Multiparticle Production." International Journal of Modern Physics A 12, no. 11 (1997): 2003–11. http://dx.doi.org/10.1142/s0217751x97001262.

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A schedule is proposed to seek a quantitative measure of nonstatistical fluctuations in high energy multiparticle production in the framework of the multifractal moments. The dynamical fluctuations are studied with two toy models representing the weak and strong correlations, respectively. A quantity, χ, is proposed to be used as the probe for the existence and to measure the size of such fluctuations.

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17

XU, MINGMEI, and LIANSHOU LIU. "ON THE DYNAMICAL FLUCTUATION OF SINGLE-EVENT TRANSVERSE MOMENTUM DISTRIBUTION." International Journal of Modern Physics A 21, no. 26 (2006): 5241–52. http://dx.doi.org/10.1142/s0217751x06032964.

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Assuming that the single-event transverse momentum distribution fluctuates event by event according to a distribution functional, we derive analytical expressions for both the variance of event-wise mean transverse momentum and the two-particle transverse momentum correlation. The relation between these two is discussed. An evaluation of statistical fluctuation is given. An exponential form for the single-event transverse momentum distribution is taken as an example to demonstrate our method for extracting event-by-event dynamical fluctuation of single-event transverse momentum distribution fr

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18

Sharif, M., and M. Zeeshan Gul. "Dynamics of spherical collapse in energy–momentum squared gravity." International Journal of Modern Physics A 36, no. 01 (2021): 2150004. http://dx.doi.org/10.1142/s0217751x21500044.

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This paper investigates the dynamics of spherical collapse in the framework of energy–momentum squared gravity. This theory overcomes the big-bang singularity and provides viable cosmological consequences in the early time universe. We proceed our work by considering the nonstatic spherically symmetric space–time in the interior and static spherically symmetric metric in the exterior regions of the star. The Darmois junction conditions between interior and exterior geometries are derived. We construct dynamical equations through the Misner–Sharp technique to analyze the impact of matter variab

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19

Choi, Joohee, Haisu Kang, Ji Hee Lee, Sung Hyun Kwon, and Seung Geol Lee. "Predicting the Properties of High-Performance Epoxy Resin by Machine Learning Using Molecular Dynamics Simulations." Nanomaterials 12, no. 14 (2022): 2353. http://dx.doi.org/10.3390/nano12142353.

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Epoxy resin is an of the most widely used adhesives for various applications owing to its outstanding properties. The performance of epoxy systems varies significantly depending on the composition of the base resin and curing agent. However, there are limitations in exploring numerous formulations of epoxy resins to optimize adhesive properties because of the expense and time-consuming nature of the trial-and-error process. Herein, molecular dynamics (MD) simulations and machine learning (ML) methods were used to overcome these challenges and predict the adhesive properties of epoxy resin. Dat

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20

FARIA DA VEIGA, PAULO A., and MICHAEL O'CARROLL. "EXACT DYNAMICAL EIGHTFOLD WAY BARYON SPECTRUM AND CONFINEMENT IN STRONGLY COUPLED LATTICE QCD." International Journal of Modern Physics A 24, no. 16n17 (2009): 3053–72. http://dx.doi.org/10.1142/s0217751x09043183.

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We obtain from the quark–gluon dynamics the eightfold way baryon spectrum exactly in an imaginary time functional integral formulation of 3+1 lattice QCD with Wilson's action in the strong coupling regime (small hopping parameter 0 < κ ≪ 1 and much smaller plaquette coupling [Formula: see text]). The model has SU(3)c local gauge and global SU(3)f flavor symmetries. A decoupling of the hyperplane method naturally unveils the form of the baryon composite fields. In the subspace of the physical Hilbert space of vectors with an odd number of quarks, the baryons are associated with isolated disp

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21

Ghosh, D., A. K. Jafry, A. Deb, et al. "Evidence of dynamical many-particle correlation in heavy-ion interactions at 60AGeV/c and 200AGeV/c." Il Nuovo Cimento A 111, no. 12 (1998): 1361–66. http://dx.doi.org/10.1007/bf03035999.

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22

CHENG, V. K. W., J. P. ROSE, and R. S. BERRY. "STRUCTURES AND DYNAMICS OF SMALL ALKALI-HALIDE CLUSTERS." Surface Review and Letters 03, no. 01 (1996): 347–51. http://dx.doi.org/10.1142/s0218625x96000632.

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The structure and phase behavior of small alkali-halide clusters were studied by constant-energy molecular dynamics and optimization. Premelting was found for ( KCl )n, n=6, 9, 12. A correlation of the energy of a number of alkali-halide clusters and their relative ionic radius was made to establish the condition for the preference of a given type of isomers as the more stable form. The isomerization dynamics of large ring-like LiBr, i.e., folding of larger rings to smaller ones with cube-like or close-packed structure, is consistent with the correlation.

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23

TIAN, JUNLONG, XIAN LI, SHIWEI YAN, XIZHEN WU, and ZHUXIA LI. "KINEMATIC CORRELATION OF THE TERNARY FISSION FOR THE SYSTEM197Au+197Au." International Journal of Modern Physics E 19, no. 02 (2010): 307–18. http://dx.doi.org/10.1142/s0218301310014777.

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Collisions of very heavy nuclei197Au +197Au at the energy of 15A MeV has been studied with the improved quantum molecular dynamics model. The experimental mass distributions of ternary fission fragments for the system197Au +197Au are reproduced well. The direct and sequential ternary fission modes are studied by the time dependent snapshots of typical ternary events. The analysis of deviation from Viola systematics indicates the nonstatistical feature of the ternary fission in these reactions.

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24

Fernández, Julio A. "The formation and dynamical survival of the comet cloud." International Astronomical Union Colloquium 83 (1985): 45–70. http://dx.doi.org/10.1017/s0252921100083792.

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AbstractThe theory of a huge reservoir of comets (the “comet cloud”) extending to almost interstellar distances is analyzed, paying special attention to its dynamical stability, formation process and orbital properties of the incoming cloud comets. The perturbing influence of passing stars and giant molecular clouds is considered. Giant molecular clouds may be an important perturbing element of the comet cloud, although they do not seem to change drastically former studies including only stellar perturbations. The more tightly bound inner portions of the comet cloud, say within 104 AU, would h

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ZALALETDINOV, ROUSTAM. "THE AVERAGING PROBLEM IN COSMOLOGY AND MACROSCOPIC GRAVITY." International Journal of Modern Physics A 23, no. 08 (2008): 1173–81. http://dx.doi.org/10.1142/s0217751x08040032.

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The averaging problem in cosmology and the approach of macroscopic gravity to resolve the problem is discussed. The averaged Einstein equations of macroscopic gravity are modified on cosmological scales by the macroscopic gravitational correlation tensor terms as compared with the Einstein equations of general relativity. This correlation tensor satisfies a system of structure and field equations. An exact cosmological solution to the macroscopic gravity equations for a constant macroscopic gravitational connection correlation tensor for a flat spatially homogeneous, isotropic macroscopic spac

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26

Hobbs, Linn W., Xianglong Yuan, L. C. Qin, Vinay Pulim, and Alexander Coventry. "The Nanostructures of Amorphous Silicas." Microscopy and Microanalysis 8, no. 1 (2002): 29–34. http://dx.doi.org/10.1017/s1431927602010061.

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Topologically modeled amorphized silica structures have been refined using a molecular dynamics simulation technique. Several metastable structures with substantially different medium-range connectivities, as characterized by primitive ring statistics, were obtained. Whereas the total correlation function is insensitive to these differences, the first sharp diffraction peak derived from energy-filtered electron diffraction shows a promising correlation to medium-range structure.

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27

Chatzidimitriou-Dreismann, C. Aris. "Quantum Beam Scattering—Beam’s Coherence Length, Which-Path Information and Weak Values." Quantum Beam Science 7, no. 3 (2023): 26. http://dx.doi.org/10.3390/qubs7030026.

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The conventional theory of neutron beams interacting with many-body systems treats the beam as a classical system, i.e., with its dynamical variables appearing in the quantum dynamics of the scattering process not as operators but only as c-numbers. Moreover, neutrons are described with plane waves, i.e., the concept of a neutron’s (finite) coherence length is here irrelevant. The same holds for electron, atom or X-ray scattering. This simplification results in the full decoupling of the probe particle’s dynamics from the quantum dynamics of the scatterer—a well-known fact also reflected in th

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28

Ekimova, Maria, Felix Hoffmann, Gul Bekcioglu-Neff, Aidan Rafferty, Erik T. J. Nibbering, and Daniel Sebastiani. "Ultrafast proton transport in water-methanol mixtures." EPJ Web of Conferences 205 (2019): 09004. http://dx.doi.org/10.1051/epjconf/201920509004.

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Femtosecond UV/IR pump-probe experiments and ab initio molecular dynamics simulations of 7-hydroxyquinoline in water-methanol mixtures demonstrate an unexpectedly dominant OH-/CH3O- transport pathway but consistent with a solvent-dependent photoacidity free energy-reactivity correlation behaviour.

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Molla, M. R., A. Z. Ziauddin Ahmed, and G. M. Bhuiyan. "Static and Dynamic Properties of Elemental Liquid Pd: An Orbital Free Molecular Dynamic Study." Journal of Nepal Physical Society 6, no. 1 (2020): 59–67. http://dx.doi.org/10.3126/jnphyssoc.v6i1.30522.

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We have studied the static and dynamic properties of liquid metal, namely Pd at thermodynamic state T=1853K within the scope of the orbital free ab-initio molecular dynamics (OF-AIMD) simulation technique. In this simulation process, electronic energy is calculated by using the Hohenberg-Kohn version of DFT. Here the electron-ion interaction energy functional is approximated by a local pseudopotential prescribed by Bhuiyan et al. The local density approximation is used to describe the exchange-correlation energy functional. The static structure factor, S(q), pair distribution function, g(r), c

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Saputra, Andrian, Karna Wijaya, Ria Armunanto, Lisa Tania, and Iqmal Tahir. "Determination of Effective Functional Monomer and Solvent for R(+)-Cathinone Imprinted Polymer Using Density Functional Theory and Molecular Dynamics Simulation Approaches." Indonesian Journal of Chemistry 17, no. 3 (2017): 516. http://dx.doi.org/10.22146/ijc.24311.

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Determination of effective functional monomer and solvent for R(+)-cathinone imprinted polymer through modeling has been done using density functional theory (DFT) and molecular dynamics (MD) simulation approaches. The selection criteria of the best monomer and solvent are based on the classical potential energy (ΔEMM) from molecular dynamics simulation and confirmed further by quantum potential energy (ΔEDFT) from DFT calculation. The DFT calculation was performed in B3LYP exchange-correlation functional within the 6-31G(d) basis set of function including Polarizable Continuum Model (PCM) sol

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Teotia, Pratibha, and Neerja Dwivedi. "In silico Identification and Optimization of Natural Inhibitors for Drug Target Sites in Cryptosporidium parvum: A Review." International Journal of Advance Research and Innovation 4, no. 4 (2016): 15–29. http://dx.doi.org/10.51976/ijari.441604.

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Cryptosporidium parvum is the most common enteric protozoan pathogens affecting humans worldwide. Currently approved drugs to treat cryptosporidiosis are ineffective and no vaccines exist against C. parvum. Here, We docked benzoxazole derivatives collected from literature with Cryptosporidium parvum inosine 5′-monophosphate dehydrogenase using AutoDock4.2 tool, which resulted in energy-based descriptors such as Binding Energy, Intermolecular Energy, Internal Energy, Torsional Energy, vdW + Hbond + desolv Energy and electrostatic energy. Molecular dynamics (MD) simulation studies were performed

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Tripathy, Sushree, Wenjun Zheng, and Anthony Auerbach. "A single molecular distance predicts agonist binding energy in nicotinic receptors." Journal of General Physiology 151, no. 4 (2019): 452–64. http://dx.doi.org/10.1085/jgp.201812212.

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Agonists turn on receptors because they bind more strongly to active (R*) versus resting (R) conformations of their target sites. Here, to explore how agonists activate neuromuscular acetylcholine receptors, we built homology models of R and R* neurotransmitter binding sites, docked ligands to those sites, ran molecular dynamics simulations to relax (“equilibrate”) the structures, measured binding site structural parameters, and correlated them with experimental agonist binding energies. Each binding pocket is a pyramid formed by five aromatic amino acids and covered partially by loop C. We fo

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Wei, Qinghua, Yingfeng Zhang, Yanen Wang, et al. "Study of the effects of water content and temperature on polyacrylamide/polyvinyl alcohol interpenetrating network hydrogel performance by a molecular dynamics method." e-Polymers 15, no. 5 (2015): 301–9. http://dx.doi.org/10.1515/epoly-2015-0087.

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AbstractAn investigation of the molecular interaction within a hydrogel system was conducted using molecular dynamics simulation, and the interaction mechanism of a polyacrylamide/polyvinyl alcohol (PAM/PVA) hydrogel system was examined specifically at the molecular level. Several characteristics of the PAM/PVA composite hydrogel system that are largely dependent on water content and temperature were studied in this paper, such as cohesive energy density, binding energy, mechanical properties and pair correlation function. The cohesive energy density and binding energy of the hydrogel system i

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Falgarone, E. "Turbulence in Interstellar Clouds." International Astronomical Union Colloquium 120 (1989): 68–79. http://dx.doi.org/10.1017/s0252921100023496.

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Above masses of the order of lOO M⊙, molecular clouds have masses and sizes which scale like those of self-gravitating polytropes bounded by an external pervading pressure. It is unlikely that this scaling is due to mere observational bias. But the physics underlying this behaviour is far from being understood. In particular, the possible contribution of turbulence to both the ambient pressure and the internal pressure (whose dependence with the density would mimic a polytropic behavior) is a difficult and much debated issue. The clouds mass, size and internal velocity dispersion are such that

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Niskanen, Johannes, Mattis Fondell, Christoph J. Sahle, et al. "Compatibility of quantitative X-ray spectroscopy with continuous distribution models of water at ambient conditions." Proceedings of the National Academy of Sciences 116, no. 10 (2019): 4058–63. http://dx.doi.org/10.1073/pnas.1815701116.

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The phase diagram of water harbors controversial views on underlying structural properties of its constituting molecular moieties, its fluctuating hydrogen-bonding network, as well as pair-correlation functions. In this work, long energy-range detection of the X-ray absorption allows us to unambiguously calibrate the spectra for water gas, liquid, and ice by the experimental atomic ionization cross-section. In liquid water, we extract the mean value of 1.74 ± 2.1% donated and accepted hydrogen bonds per molecule, pointing to a continuous-distribution model. In addition, resonant inelastic X-ra

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Niu, Cong, You-zhi Hao, Dao-lun Li, and De-tang Lu. "Second-Order Gas-Permeability Correlation of Shale During Slip Flow." SPE Journal 19, no. 05 (2014): 786–92. http://dx.doi.org/10.2118/168226-pa.

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Summary Recent molecular-dynamics (MD) simulation of methane flow through nanoscale kaolinite channels shows that the gas molecules accumulate near the kaolinite wall, which will reduce the flowpath of the gas through tight porous media. Considering this gas-accumulation effect, and on the basis of the corrected second-order slip boundary condition (BC) proposed by Zhang et al. (2010), a permeability-correlation model is proposed for nanoscale flow in highly compacted shale reservoirs. Full-derivation detail of this model is presented along with a comparison with several existing correlations.

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Ali, Hafiz Saqib, Arghya Chakravorty, Jas Kalayan, Samuel P. de Visser, and Richard H. Henchman. "Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge." Journal of Computer-Aided Molecular Design 35, no. 8 (2021): 911–21. http://dx.doi.org/10.1007/s10822-021-00406-5.

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AbstractFree energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy–entropy (EE) method to calculate the host–guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses forc

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Nicholson, Donald M., C. Y. Gao, Marshall T. McDonnell, Clifton C. Sluss, and David J. Keffer. "Entropy Pair Functional Theory: Direct Entropy Evaluation Spanning Phase Transitions." Entropy 23, no. 2 (2021): 234. http://dx.doi.org/10.3390/e23020234.

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We prove that, within the class of pair potential Hamiltonians, the excess entropy is a universal, temperature-independent functional of the density and pair correlation function. This result extends Henderson’s theorem, which states that the free energy is a temperature dependent functional of the density and pair correlation. The stationarity and concavity of the excess entropy functional are discussed and related to the Gibbs–Bugoliubov inequality and to the free energy. We apply the Kirkwood approximation, which is commonly used for fluids, to both fluids and solids. Approximate excess ent

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Lai, Fang-I., Jui-Fu Yang, Woei-Tyng Lin, Wei-Chun Chen, Yu-Chao Hsu, and Shou-Yi Kuo. "Correlation of Morphology Evolution with Carrier Dynamics in InN Films Heteroepitaxially Grown by MOMBE." Catalysts 11, no. 8 (2021): 886. http://dx.doi.org/10.3390/catal11080886.

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In this study, we report the catalyst-free growth of n-type wurtzite InN, along with its optical properties and carrier dynamics of different surface dimensionalities. The self-catalyzed epitaxial growth of InN nanorods grown by metal–organic molecular-beam epitaxy on GaN/Al2O3(0001) substrates has been demonstrated. The substrate temperature is dominant in controlling the growth of nanorods. A dramatic morphological change from 2D-like to 1D nanorods occurs with decreasing growth temperature. The InN nanorods have a low dislocation density and good crystalline quality, compared with InN films

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Galametz, Maud, Anaëlle Maury, Josep M. Girart, et al. "An observational correlation between magnetic field, angular momentum and fragmentation in the envelopes of Class 0 protostars?" Astronomy & Astrophysics 644 (December 2020): A47. http://dx.doi.org/10.1051/0004-6361/202038854.

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Aims. The main goal of the following analysis is to assess the potential role of magnetic fields in regulating the envelope rotation, the formation of disks and the fragmentation of Class 0 protostars in multiple systems. Methods. We use the Submillimeter Array to carry out observations of the dust polarized emission at 0.87 mm, in the envelopes of a large sample of 20 Class 0 protostars. We estimate the mean magnetic field orientation over the central 1000 au envelope scales to characterize the orientation of the main component of the organized magnetic field at the envelope scales in these e

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Heshmatpour, Constantin, Jürgen Hauer, and František Šanda. "Correlated spectral fluctuations quantified by line shape analysis of fifth-order two-dimensional electronic spectra." Journal of Chemical Physics 156, no. 8 (2022): 084114. http://dx.doi.org/10.1063/5.0081053.

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Correlated spectral fluctuations were suggested to coordinate excitation transport inside natural light harvesting complexes. We demonstrate the capacities of 2D line shapes from fifth-order coherent electronic signals (R5-2D) to report on such fluctuations in molecular aggregates and present a stochastic approach to fluctuations in correlated site and bi-exciton binding energies in the optical dynamics of Frenkel excitons. The model is applied to R5-2D line shapes of a homodimer, and we show that the peak tilt dynamics are a measure for site energy disorder, inter-site correlation, and the st

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Cao, Xingjian, Yongtai Pan, Chuan Zhang, et al. "Molecular Dynamics Study on Crack Angle Effect on Amorphous Silica Fracture Performance." Minerals 13, no. 8 (2023): 1068. http://dx.doi.org/10.3390/min13081068.

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To investigate the effect of crack angle on the fracture performance of brittle materials under tensile load, a molecular dynamics simulation method based on ReaxFF is used to establish an amorphous silica model through the high-temperature melting and annealing process. Under the simulation environment of 300 K, 1.013 × 105 Pa and 5 × 109 s−1, the impact of crack angle on the fracture performance of the model from three perspectives is analyzed: material mechanical properties, micro fracture process, and energy evolution. The result indicates that as the crack angle increases, the ultimate st

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Li, Shenshen, and Jijun Xiao. "Molecular Dynamics Simulations for Effects of Fluoropolymer Binder Content in CL-20/TNT Based Polymer-Bonded Explosives." Molecules 26, no. 16 (2021): 4876. http://dx.doi.org/10.3390/molecules26164876.

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In order to better understand the role of binder content, molecular dynamics (MD) simulations were performed to study the interfacial interactions, sensitivity and mechanical properties of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/2,4,6-trinitrotoluene (CL-20/TNT) based polymer-bonded explosives (PBXs) with fluorine rubber F2311. The binding energy between CL-20/TNT co-crystal (1 0 0) surface and F2311, pair correlation function, the maximum bond length of the N–NO2 trigger bond, and the mechanical properties of the PBXs were reported. From the calculated binding energy, it wa

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Jayadas, N. H., and K. Prabhakaran Nair. "Study of the Anti-Wear Properties of Coconut Oil Using Quantum Chemical Calculations and Tribological Tests." Journal of Tribology 128, no. 3 (2006): 654–59. http://dx.doi.org/10.1115/1.2197853.

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In this paper Spartan 02, a molecular dynamics software, is used to analyze and predict the tribological properties of coconut oil in a qualitative manner on the basis of carbon chain length of the constituent fatty acids, their polarity (net electrostatic charge, Qr), the energies of the molecular orbitals E_HOMO (energy of the highest occupied molecular orbital), and E_LUMO (energy of the lowest unoccupied molecular orbital), and the heats of formations (H-Form) of the iron soaps of respective fatty acids. Tribological properties of the constituent fatty acids of coconut oil were evaluated u

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Mali, Provash, Soumya Sarkar, Amitabha Mukhopadhyay, and Gurmukh Singh. "Wavelet Analysis of Shower Track Distribution in High-Energy Nucleus-Nucleus Collisions." Advances in High Energy Physics 2013 (2013): 1–13. http://dx.doi.org/10.1155/2013/759176.

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A continuous wavelet analysis is performed for pattern recognition of charged particle emission data in28Si-Ag/Br interaction at 14.5A GeV and in32S-Ag/Br interaction at 200A GeV. Making use of the event-wise local maxima present in the scalograms, we try to identify the collective behavior in multiparticle production, if there is any. For the first time, the wavelet results are compared with a model prediction based on the ultrarelativistic quantum molecular dynamics (UrQMD), where we adopt a charge reassignment algorithm to modify the UrQMD events to mimic the Bose-Einstein type of correlati

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Lee, One-Sun. "Dynamic Properties of Water Confined in Graphene-Based Membrane: A Classical Molecular Dynamics Simulation Study." Membranes 9, no. 12 (2019): 165. http://dx.doi.org/10.3390/membranes9120165.

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We performed molecular dynamics simulations of water molecules inside a hydrophobic membrane composed of stacked graphene sheets. By decreasing the density of water molecules inside the membrane, we observed that water molecules form a droplet through a hydrogen bond with each other in the hydrophobic environment that stacked graphene sheets create. We found that the water droplet translates as a whole body rather than a dissipate. The translational diffusion coefficient along the graphene surface increases as the number of water molecules in the droplet decreases, because the bigger water dro

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BYKHOVSKI, ALEXEI, TATIANA GLOBUS, TATYANA KHROMOVA, BORIS GELMONT, and DWIGHT WOOLARD. "AN ANALYSIS OF THE THZ FREQUENCY SIGNATURES IN THE CELLULAR COMPONENTS OF BIOLOGICAL AGENTS." International Journal of High Speed Electronics and Systems 17, no. 02 (2007): 225–37. http://dx.doi.org/10.1142/s012915640700445x.

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The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated an

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BLASCHKE, D., G. BURAU, YU L. KALINOVSKY, P. MARIS, and P. C. TANDY. "FINITE T MESON CORRELATIONS AND QUARK DECONFINEMENT." International Journal of Modern Physics A 16, no. 12 (2001): 2267–91. http://dx.doi.org/10.1142/s0217751x01003457.

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The finite temperature spatial [Formula: see text] correlation modes in the π and ρ channels are studied with the rainbow-ladder truncated quark Dyson–Schwinger equation and Bethe–Salpeter equation in the Matsubara formalism. To retain the finite range of the effective interaction while facilitating summation over fermion Matsubara modes necessary to ensure continuity at T=0, a separable kernel is used. The model is fixed by T=0 properties and it implements dynamical chiral symmetry breaking and quark confinement. Transition temperatures for deconfinement (Td) and chiral restoration (Tc) are i

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Chen, Jianzhong, Xingyu Wang, Laixue Pang, John Z. H. Zhang, and Tong Zhu. "Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations." Nucleic Acids Research 47, no. 13 (2019): 6618–31. http://dx.doi.org/10.1093/nar/gkz499.

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Abstract Riboswitches can regulate gene expression by direct and specific interactions with ligands and have recently attracted interest as potential drug targets for antibacterial. In this work, molecular dynamics (MD) simulations, free energy perturbation (FEP) and molecular mechanics generalized Born surface area (MM-GBSA) methods were integrated to probe the effect of mutations on the binding of ligands to guanine riboswitch (GR). The results not only show that binding free energies predicted by FEP and MM-GBSA obtain an excellent correlation, but also indicate that mutations involved in t

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Березин, К. В., К. Н. Дворецкий, М. Л. Чернавина та ін. "Оптическое просветление кожи человека in vivo рядом моносахаридов". Журнал технической физики 127, № 8 (2019): 329. http://dx.doi.org/10.21883/os.2019.08.48051.29-19.

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AbstractWe present the results of in vivo optical immersion clearing of human skin by aqueous solutions of some immersion agents (ribose, glucose, and fructose monosaccharides and glycerol), obtained using optical coherence tomography (OCT). To assess the efficiency of optical clearing, we determined the values of the rate of change of the light scattering coefficient, obtained using the averaged A-scan of the OCT signal in the derma section at a depth of 350–700 μm. A good correlation was observed between the rate of change of the light scattering coefficient and the potential of the optical

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