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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 (July 2014): 073301. http://dx.doi.org/10.1088/1674-1056/23/7/073301.
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HWA, RUDOLPH C. "GEOMETRICAL AND DYNAMICAL MULTIPLICITY FLUCTUATIONS IN HIGH-ENERGY NUCLEAR COLLISIONS." International Journal of Modern Physics A 04, no. 02 (January 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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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 (September 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 finite-temperature correlation functions, and extension to systems obeying Bose statistics is possible. Accelerated convergence is achieved via Monte Carlo or molecular dynamics sampling techniques and through the construction of improved imaginary time propagators. The accuracy of the methodology is demonstrated on several model systems, including models of Bose and Fermi particles. Applications to liquid argon, neon and para-hydrogen are presented.
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PAPA, M., and G. GIULIANI. "DYNAMICAL CORRELATIONS AND THE SYMMETRY INTERACTION." International Journal of Modern Physics E 17, no. 10 (November 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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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 (May 10, 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 such relationship. Analytic and numerical simulations demonstrate that if an initial state is taken to be the stretch- or the bend-vibrationally localized state, the mutual information, the Pauli entropy, and the concurrence are dominant-positively correlated while they are dominantly anti-correlated with the interacting energy among three anharmonic vibrational modes. In particular, such correlation is more distinct for the localized state with high excitations in the bending mode. The nice quasi-periodicity of those quantities in D2O molecule reveals that this molecule prepared in the localized state in the stretching or the bending mode can be more appreciated for molecular quantum computation. However, the dynamical correlations of those quantities behave irregularly for the dislocalized states. Moreover, the hierarchy of the mutual information and the Pauli entropy is explicitly proved. Quantum entropy and energy in every vibrational mode are investigated. Thereby, the relation between bipartite and tripartite entanglements is discussed as well. Those are useful for the understanding of quantum correlations in high-dimensional states in polyatomic molecules from quantum information and intramolecular dynamics.
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Finn, Molly K., Remy Indebetouw, Kelsey E. Johnson, Allison H. Costa, C. H. Rosie Chen, Akiko Kawamura, Toshikazu Onishi, et al. "Structural and Dynamical Analysis of the Quiescent Molecular Ridge in the Large Magellanic Cloud." Astronomical Journal 164, no. 2 (July 21, 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 significantly lower kinetic energy at a given size scale and also lower surface densities than the other regions, resulting in higher virial parameters. This suggests that the Ridge is not forming massive stars as actively as the other regions because it has less dense gas and not because collapse is suppressed by excess kinetic energy. We also find that these physical conditions and energy balance vary significantly within the Ridge and that this variation appears only weakly correlated with distance from sites of massive-star formation such as R136 in 30 Dor, which is ∼1 kpc away. These variations also show only a weak correlation with local star formation activity within the clouds.
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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 equations of motion. Dynamics of different isomers of the Li9+ cluster have been investigated as a function of excess energy. It is shown that different isomers, even those similar in energy, can exhibit different structural and dynamical behavior. The analysis of the simulations leads to the conclusion that structures with a central atom, in particular the centered antiprism of Li9+ exhibit concerted mobility of the peripheral atoms at relatively low excess energy. In contrast, compact tetrahedral type structures show much more rigid behavior at low excess energy. However, the former ones need larger excess of internal energy to undergo isomerizations to geometrically different structures than the latter ones. At the time scale of our simulations we found that for the intermediate excess energies it is "easier" to carry the cluster in the basin of the lowest energy isomer than in the reverse direction. It has been found that the liquid-like behavior in small Li clusters becomes apparent at relatively high temperature in spite of large mobility of their atoms.
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Kiselev, S. M. "Azimuthal multiparticle correlations in high-energy heavy-ion collisions in the molecular-dynamical model." Physics Letters B 216, no. 3-4 (January 1989): 262–66. http://dx.doi.org/10.1016/0370-2693(89)91112-x.
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Comes, F. J. "Vector Correlations in Molecular Photofragmentations." Laser Chemistry 11, no. 3-4 (January 1, 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” from the line shapes. Information on the unstable intermediate state is gained from the stable fragments long after the dissociation of the parent molecule. In particular, information on the “lifetime” of the intermediate on a femtosecond time scale can be obtained.A number of molecules, mainly three and four atomic, have been studied by this technique. Hydrogen peroxide has shown up as a textbook example. A complete analysis was possible including not only correlation of different types of fragment motion but also a correlation of the two coincident particles formed from the same parent molecule. The experimental results are in full agreement with recent calculations of the dynamics of the fragmentation on newly obtained potential energy surfaces. Hydrogen peroxide shows a strong dependence of its potential energy on the dihedral angle in the two electronic states amenable to laser excitation. This experiment further demonstrates that an analysis is also possible if two states are excited simultaneously.Another good example is the fragmentation of hydrazoic acid for which also coincident pair correlation has been treated. Here again the results agree excellently with a qualitative picture which can be drawn from recently calculated ab initio potential energy surfaces. The HN3 example is much more complicated than the former one due to its higher structured upper potential energy surface. Strong rotational excitation is observed in the N2 fragment leaving the NH fragment rotationally cold.The treatment of vector correlations in molecular photofragmentation is a powerful tool for the study of the dynamics of molecular dissociation reactions.
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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 (August 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 the degree of space-momentum correlations at this energy. The results are useful to the designing the hadron detector at CSR.
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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 (February 16, 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 stellar disk and a nuclear stellar cluster as observed from our Galaxy. The wandering distance of the black hole in the gravitational potential of the nuclear bulge is evaluated to get as large as several 10 pc, when the black hole mass is relatively small. The distance, however, shrinks as the black hole mass increases, and the equilibrium solution between the energy gain and loss disappears when the black hole mass exceeds an upper limit. As a result, we can expect the following scenario for the evolution of the black hole mass: When the black hole mass is smaller than the upper limit, mass accretion of the interstellar matter in the circumnuclear region, causing the AGN activities, makes the black hole mass larger. However, when the mass gets to the upper limit, the black hole loses the balancing force against the dynamical friction and starts spiraling downward to the gravity center. From simple parameter scaling, the upper mass limit of the black hole is found to be proportional to the bulge mass, and this could explain the observed correlation of the black hole mass with the bulge mass.
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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 (July 24, 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. By varying the external gravitational potential, we probe galactic-dynamical environments spanning an order of magnitude in the orbital angular velocity, gravitational stability, mid-plane pressure, and the gradient of the galactic rotation curve. The simulated molecular clouds are highly overdense (∼100×) and overpressured (∼25×) relative to the ambient interstellar medium. Their gravoturbulent and star-forming properties are decoupled from the dynamics of the galactic mid-plane, so that the kpc-scale star formation rate surface density is related only to the number of molecular clouds per unit area of the galactic mid-plane. Despite this, the clouds display clear, statistically significant correlations of their rotational properties with the rates of galactic shearing and gravitational free-fall. We find that galactic rotation and gravitational instability can influence their elongation, angular momenta, and tangential velocity dispersions. The lower pressures and densities of the H i clouds allow for a greater range of significant dynamical correlations, mirroring the rotational properties of the molecular clouds, while also displaying a coupling of their gravitational and turbulent properties to the galactic-dynamical environment.
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Huang, Kaisheng, Yi Liu, Shuixiu Wen, Yuxin Zhao, Hanjing Ding, Hui Liu, and De-Xin Kong. "Binding Mechanism of CD47 with SIRPα Variants and Its Antibody: Elucidated by Molecular Dynamics Simulations." Molecules 28, no. 12 (June 7, 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 (B6H12.2). The calculated binding free energy of CD47-B6H12.2 is lower than that of CD47-SIRPαv1 and CD47-SIRPαv2 in all the three simulations, indicating that CD47-B6H12.2 has a higher binding affinity than the other two complexes. Moreover, the dynamical cross-correlation matrix reveals that the CD47 protein shows more correlated motions when it binds to B6H12.2. Significant effects were observed in the energy and structural analyses of the residues (Glu35, Tyr37, Leu101, Thr102, Arg103) in the C strand and FG region of CD47 when it binds to the SIRPα variants. The critical residues (Leu30, Val33, Gln52, Lys53, Thr67, Arg69, Arg95, and Lys96) were identified in SIRPαv1 and SIRPαv2, which surround the distinctive groove regions formed by the B2C, C’D, DE, and FG loops. Moreover, the crucial groove structures of the SIRPα variants shape into obvious druggable sites. The C’D loops on the binding interfaces undergo notable dynamical changes throughout the simulation. For B6H12.2, the residues Tyr32LC, His92LC, Arg96LC, Tyr32HC, Thr52HC, Ser53HC, Ala101HC, and Gly102HC in its initial half of the light and heavy chains exhibit obvious energetic and structural impacts upon binding with CD47. The elucidation of the binding mechanism of SIRPαv1, SIRPαv2, and B6H12.2 with CD47 could provide novel perspectives for the development of inhibitors targeting CD47-SIRPα.
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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 (July 14, 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 order parameter differs significantly for heteronuclear admixtures. We evaluate the fidelity as a figure of merit for the overlap between the order parameters of each atomic species. Dynamical evidence of the differences between the phases of the order parameters is predicted to manifest in their corresponding linear and angular momenta. We numerically verify that the total angular and linear momenta are both conserved during the collision. Some direct correlations between the Weber number and the impact parameter with the distribution of the dynamical variables are established.
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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 (May 17, 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 Stress Related 1 (LHCSR1) is the protein responsible for quenching in moss. Here, we expand an analysis of the correlation function of the fluorescence lifetime by improving the estimation of the lifetime states and by developing a multicomponent model correlation function, and we apply this analysis at the single-molecule level. Through these advances, we resolve previously hidden rapid dynamics, including multiple parallel processes. By applying this technique to LHCSR1, we identify and quantitate parallel dynamics on hundreds of microseconds and tens of milliseconds timescales, likely at two quenching sites within the protein. These sites are individually controlled in response to fluctuations in sunlight, which provides robust regulation of the light-harvesting machinery. Considering our results in combination with previous structural, spectroscopic, and computational data, we propose specific pigments that serve as the quenching sites. These findings, therefore, provide a mechanistic basis for quenching, illustrating the ability of this method to uncover protein function.
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Yang, C. B., and X. Cai. "Quantitative Measure of Dynamical Fluctuations in Multiparticle Production." International Journal of Modern Physics A 12, no. 11 (April 30, 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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XU, MINGMEI, and LIANSHOU LIU. "ON THE DYNAMICAL FLUCTUATION OF SINGLE-EVENT TRANSVERSE MOMENTUM DISTRIBUTION." International Journal of Modern Physics A 21, no. 26 (October 20, 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 from experimental data.
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Sharif, M., and M. Zeeshan Gul. "Dynamics of spherical collapse in energy–momentum squared gravity." International Journal of Modern Physics A 36, no. 01 (January 10, 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 variables and dark source terms on the collapsing phenomenon. A correlation among dark source terms, Weyl scalar and matter variables is also established. Due to the presence of multivariate function and its derivatives, space–time is no longer considered to be conformally flat. To obtain conformally flat space–time, we have considered a particular model of this gravity which yields conformally flat space–time and homogeneity of the energy density through the entire system. We conclude that positive dark source terms as well as negative pressure gradient provide the anti-gravitational behavior leading to the stability of self-gravitating objects and hence prevent the collapsing process.
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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 (July 9, 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. Datasets for diverse epoxy adhesive formulations were constructed by considering the degree of crosslinking, density, free volume, cohesive energy density, modulus, and glass transition temperature. A linear correlation analysis demonstrated that the content of the curing agents, especially dicyandiamide (DICY), had the greatest correlation with the cohesive energy density. Moreover, the content of tetraglycidyl methylene dianiline (TGMDA) had the highest correlation with the modulus, and the content of diglycidyl ether of bisphenol A (DGEBA) had the highest correlation with the glass transition temperature. An optimized artificial neural network (ANN) model was constructed using test sets divided from MD datasets through error and linear regression analyses. The root mean square error (RMSE) and correlation coefficient (R2) showed the potential of each model in predicting epoxy properties, with high linear correlations (0.835–0.986). This technique can be extended for optimizing the composition of other epoxy resin systems.
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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 (July 10, 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 dispersion curves in the energy–momentum spectrum. Spectral representations are derived for the two-baryon correlations, which allow us to detect the energy–momentum spectrum and particles as complex momentum space singularities. The spin 1/2 octet and spin 3/2 decuplet baryons have asymptotic mass -3ln κ and for each baryon there is an antibaryon with identical spectral properties. An auxiliary function method is used to obtain convergent expansions for the masses after subtracting the singular part -3ln κ. The nonsingular part of the mass is analytic in κ and β, i.e. the expansions are controlled to all orders. For β = 0, all the masses have the form M = -3ln κ - 3κ3/4 + κ6r(κ), with r(κ) real analytic. Although we have no Lorentz symmetry in our lattice model, we show that there is a partial restoration of the continuous rotational symmetry at zero spatial momentum, which implies that for all members of the octet (decuplet) r(κ) is the same. So, there is no mass splitting within the octet and within the decuplet. However, there is an octet–decuplet mass difference of [Formula: see text] at β = 0; the splitting persists for β ≠ 0. We also obtain the (anti)baryon dispersion curves which admit the representation [Formula: see text], where [Formula: see text] and [Formula: see text] is of [Formula: see text]. For the octet, [Formula: see text] is jointly analytic in κ and in each pj, for small [Formula: see text]. A new local symmetry, which we call spin flip, is used to establish constraints for the matrix-valued two-baryon correlation and show that all the octet dispersion curves are the same and that the four decuplet dispersion curves are pairwise-identical and depend only on the modulus of the spin z-component. Using a correlation subtraction method we show that the spectrum generated by the baryon and antibaryon fields is the only spectrum, in the odd quark subspace of physical states, up to near the baryon–meson threshold of ≈ -5ln κ. Combining this result with a similar result for the mesons, with mass ≈ -2ln κ, shows that the only spectrum in the entire space of states, up to near the two-meson threshold of ≈ -4ln κ, is generated by the eightfold way hadrons. Hence, for 0 < κ ≪ β ≪ 1, we have shown confinement up to near this threshold.
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Ghosh, D., A. K. Jafry, A. Deb, R. Chattopadhyay, S. Das, M. Lahiri, B. Biswas, K. Purkait, S. Das, and J. Roychoudhury. "Evidence of dynamical many-particle correlation in heavy-ion interactions at 60AGeV/c and 200AGeV/c." Il Nuovo Cimento A 111, no. 12 (December 1998): 1361–66. http://dx.doi.org/10.1007/bf03035999.
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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 (February 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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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 (February 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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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 have withstood the disrupting forces over the age of the solar system. The theory of a primordial comet origin in the outer planetary region close to Neptune’s orbit is specially analyzed. A primordial comet origin is consistent with the cosmogonic view that a large amount of residual material was ejected during the last stage in the formation of the Jovian planets. The smooth diffusion in the energy space of bodies scattered by Neptune guarantees that most of them will fall in the narrow range of energies close to zero (near-parabolic orbits) where passing stars and GMCs can act effectively on them. The long time scales of ~109 yr required for bodies scattered by Neptune to reach near-parabolic orbits would indicate that the buildup of the comet cloud was an event that took place long after the planets formed. Depending on the field of perturbing galactic objects, it is possible to conceive that most scattered comets were stored in rather tightly bound orbits (a ~l04 AU), favoring the concept of their dynamical survival over several billion yr. Alternative theories of comet cloud formation, e.g. in-situ origin or interstellar capture, are also discussed. The main difficulty of the in-situ theory is to explain how comets could accumulate at large heliocentric distances where the density of the nebular material was presumably very low. The interstellar capture theory also meets severe dynamical objections as, for instance, the lack of observed comets with original strongly hyperbolic orbits and the extremely low probability of capture under most plausible conditions. Since our knowledge of the structure of giant molecular clouds and their frequency of encounters with the solar system is still very uncertain, the concept of capture of transient comet clouds during such encounters can be advanced very little beyond the speculative stage. Some other dynamical properties of relevance to theories of origin and structure of the comet cloud are also reviewed. We mention, for instance, the distribution of perihelion points on the celestial sphere. There seems to be here a well established deviation from randomness, although the debate on whether or not there is a preference of the perihelion clustering for the vicinity of the apex of the solar motion is still unsettled. The alleged correlation with the solar apex may be biased by the preference of comet discoveries in the northern hemisphere. Deviations from randomness might be caused by very close stellar passages in the recent past. The excess of retrograde orbits among the observed “new” and young comets - mainly those with q ≳ 2 AU - is another well known dynamical feature. Such an excess may probably be accounted for by the combined action of planetary and stellar perturbations. Because of the decreasing action of planetary perturbations with increasing heliocentric distances, a significant increase in the rate of passages of long-period comets is predicted for the outer planetary region.
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ZALALETDINOV, ROUSTAM. "THE AVERAGING PROBLEM IN COSMOLOGY AND MACROSCOPIC GRAVITY." International Journal of Modern Physics A 23, no. 08 (March 30, 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 space-time is presented. The correlation tensor term in the macroscopic Einstein equations has been found to take the form of either a negative or positive spatial curvature term. Thus, macroscopic gravity provides a cosmological model for a flat spatially homogeneous, isotropic Universe which obeys the dynamical law for either an open or closed Universe.
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Hobbs, Linn W., Xianglong Yuan, L. C. Qin, Vinay Pulim, and Alexander Coventry. "The Nanostructures of Amorphous Silicas." Microscopy and Microanalysis 8, no. 1 (February 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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Chatzidimitriou-Dreismann, C. Aris. "Quantum Beam Scattering—Beam’s Coherence Length, Which-Path Information and Weak Values." Quantum Beam Science 7, no. 3 (August 15, 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 the standard formalism of time-correlation functions (see textbooks). Making contact with modern quantum-theoretical approaches (e.g., quantum entanglement, “which-path information” versus interference, von Neumann measurement, Weak Values (WV), etc.), new observable effects of non-relativistic quantum beam scattering may be exposed and/or predicted, for instance, a momentum-transfer deficit and an intensity deficit in neutron scattering from protons of hydrogen-containing samples. A new WV-theoretical treatment is provided, which explains both these “deficit effects” from first principles and on equal footing.
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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 (August 6, 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), coordination number, Nc, and isothermal compressibility, κT, are studied which are familiar as static properties. The single particle and collective dynamics namely diffusion coefficient, dynamic structure factor, velocity of sound, shear viscosity etc. are also studied. The results of calculation agree well with experimental as well as other theoretical values.
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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 (November 30, 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) solvation effect. From this research, it is obtained that N,N’-methylene bis acrylamide and chloroform are respectively the best candidates for effective functional monomer and solvent, for the synthesis of R(+)-cathinone imprinted polymer.
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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 through the NAMD graphical user interface embedded in visual molecular dynamics. After that, we have built quantitative structure activity relationship (QSAR) model using energy-based descriptors yielding correlation coefficient r2 of 0.7948. To assess the predictive performance of QSAR model, different cross-validation procedures were adopted. Our results suggests that ligand-receptor binding interactions for inosine 5′-monophosphate dehydrogenase employing QSAR modeling seems to be a promising approach to design more potent inosine 5′-monophosphate dehydrogenase inhibitors prior to their synthesis.
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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 (January 11, 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 found that in R* versus R, loop C is displaced outward, the pocket is smaller and skewed, the agonist orientation is reversed, and a key nitrogen atom in the agonist is closer to the pocket center (distance dx) and a tryptophan pair but farther from αY190. Of these differences, the change in dx shows the largest correlation with experimental binding energy and provides a good estimate of agonist affinity, efficacy, and efficiency. Indeed, concentration–response curves can be calculated from just dx values. The contraction and twist of the binding pocket upon activation resemble gating rearrangements of the extracellular domain of related receptors at a smaller scale.
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Wei, Qinghua, Yingfeng Zhang, Yanen Wang, Weihong Chai, Mingming Yang, Wenxiao Zeng, and Meng Wang. "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 (September 1, 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 increased with higher water content. Results also showed that increased temperatures led to a decrease in the cohesive energy density of the system, while binding energy remained unchanged. The mechanical properties of the system were evaluated by analyzing the static mechanic performance. Results showed that elastic coefficients, engineering modulus and ductility decreased with increasing water content and temperature. In addition, analysis of the pair correlation function revealed mainly hydrogen bonding interactions between H2O molecules and surrounding atoms or functional groups. Results also indicated that the strength of these hydrogen bonds was Owater>OPVA>OPAM>NPAM, confirming both the potential and the difficulty of hydrogen bond formation. The aforementioned findings help in understanding the interaction mechanisms between the components of a hydrogel system and in demonstrating the effects of water content and temperature on the PAM/PVA hydrogel system, which provides useful information on the possible operating windows of a biomedical hydrogel-making process.
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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 they are observed to be in approximate virial balance between their self-gravity, the surface energy term due to the ambient pressure and their internal energy. The latter is dominated by the kinetic energy of disordered internal motions. However, there has been little evidence so far that these motions are actually turbulent rather than simply disordered. The transition to turbulence in a flow occurs when the non linear advection term in the momentum equation, v.Δv, considerably exceeds the viscous dissipation term, vΔv (where v is the kinematic viscosity). Non linearities therefore dominate the physics of a turbulent flow and the velocities are not randomly distributed. Most of the previous attempts to determine a well-defined correlation length in the velocity field (Kleiner and Dickman 1985, a and b; Scalo 1984), which is predicted to be close to the scale at which the energy is injected, or to characterize the expected hierarchical structure (Pérault et al. 1986) have been plagued by the lack of dynamical range in the data set and the range of scales over which the correlation functions have been computed. The most plausible determination, that of Kleiner and Dickman (1987) who claim to have found a correlation length of 0.2 pc in the Taurus cloud, gives a result which is so close to the angular resolution of the observations that it is doubtful.
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Niskanen, Johannes, Mattis Fondell, Christoph J. Sahle, Sebastian Eckert, Raphael M. Jay, Keith Gilmore, Annette Pietzsch, 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 (February 19, 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-ray scattering with unprecedented energy resolution also supports continuous distribution of molecular neighborhoods within liquid water, as do X-ray emission spectra once the femtosecond scattering duration and proton dynamics in resonant X-ray–matter interaction are taken into account. Thus, X-ray spectra of liquid water in ambient conditions can be understood without a two-structure model, whereas the occurrence of nanoscale-length correlations within the continuous distribution remains open.
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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 (March 10, 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. Results show that, with the increase of the Knudsen number (Kn), the molecular-accumulation effect has an obvious negative effect on the shale permeability, which should not be neglected in further investigation. The parametric investigation of the model proposed shows that the permeability is mostly decided by the pore-wall structure of shale matrix and only slightly influenced by the gas property.
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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 (July 15, 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 force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host–guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) “Drugs of Abuse” Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol−1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.
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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 (February 17, 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 entropy functionals are developed and compared to results from thermodynamic integration. The pair functional approach gives the absolute entropy and free energy based on simulation output at a single temperature without thermodynamic integration. We argue that a functional of the type, which is strictly applicable to pair potentials, is also suitable for first principles calculation of free energies from Born–Oppenheimer molecular dynamics performed at a single temperature. This advancement has the potential to reduce the evaluation the free energy to a simple modification to any procedure that evaluates the energy and the pair correlation function.
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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 (July 22, 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. In terms of optical properties, the nanorod structure exhibits strong recombination of Mahan excitons in luminescence, and an obvious spatial correlation effect in phonon dispersion. The downward band structure at the nanorod surface leads to the photon energy-dependent lifetime being upshifted to the high-energy side.
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Galametz, Maud, Anaëlle Maury, Josep M. Girart, Ramprasad Rao, Qizhou Zhang, Mathilde Gaudel, Valeska Valdivia, 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 embedded protostars. This direction is compared to that of the protostellar outflow in order to study the relation between their misalignment and the kinematics of the circumstellar gas. The latter is traced via velocity gradient observed in the molecular line emission (mainly N2H+) of the gas at intermediate envelope scales. Results. We discover a strong relationship between the misalignment of the magnetic field orientation with the outflow and the amount of angular momentum observed at similar scales in the protostellar envelope, revealing a potential link between the kinetic and the magnetic energy at envelope scales. The relation could be driven by favored B-misalignments in more dynamical envelopes or a dependence of the envelope dynamics with the large-scale B initial configuration. Comparing the trend with the presence of fragmentation, we observe that single sources are mostly associated with conditions of low angular momentum in the inner envelope and good alignment of the magnetic field with protostellar outflows, at intermediate scales. Our results suggest that the properties of the magnetic field in protostellar envelopes bear a tight relationship with the rotating-infalling gas directly involved in the star and disk formation: we find that it may not only influence the fragmentation of protostellar cores into multiple stellar systems, but also set the conditions establishing the pristine properties of planet-forming disks.
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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 (February 28, 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 strength of bi-exciton binding energy fluctuations.
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Cao, Xingjian, Yongtai Pan, Chuan Zhang, Yankun Bi, Pengfei Liu, Congcong Wang, and Chenjie Tang. "Molecular Dynamics Study on Crack Angle Effect on Amorphous Silica Fracture Performance." Minerals 13, no. 8 (August 11, 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 strain and stress of the model decrease accordingly. The crack propagation path of the model will exhibit a “Z” shape due to the coupling effect of tensile and shear stress. The elastic energy efficiency and new surface energy efficiency of the model increase with the increase in crack angle, and the most new surface is generated at 45° crack angle. The linear regression model and asymptotic regression model are used to fit the trends of elastic energy efficiency and new surface energy efficiency with crack angle, respectively, with correlation coefficients R2 of 0.986 and 0.994. In the actual comminution process, the input energy required for crushing as well as the surface area and morphology of the material after crushing can be changed by adjusting the angle between the load and the main crack of the material being broken.
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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 (August 12, 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 was found that binding energy increases with increasing F2311 content. Additionally, according to the results of pair correlation function, it turns out that H–O hydrogen bonds and H–F hydrogen bonds exist between F2311 molecules and the molecules in CL-20/TNT. The length of trigger bond in CL-20/TNT were adopted as theoretical criterion of sensitivity. The maximum bond length of the N–NO2 trigger bond decreased very significantly when the F2311 content increased from 0 to 9.2%. This indicated increasing F2311 content can reduce sensitivity and improve thermal stability. However, the maximum bond length of the N–NO2 trigger bond remained essentially unchanged when the F2311 content was further increased. Additionally, the calculated mechanical data indicated that with the increase in F2311 content, the rigidity of CL-20/TNT based PBXs was decrease, the toughness was improved.
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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 (February 15, 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 using a four-ball tester as per ASTM D4172 method. The experimental results showed good correlation to the selected quantum chemical descriptors. The influence of an anti-wear additive on the tribological performance of coconut oil and the optimum additive concentration were also evaluated experimentally.
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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 correlation among identical mesons—a feature known to be the most dominating factor responsible for local cluster formation. Statistically significant deviations between the experiment and the simulation are interpreted in terms of nontrivial dynamics of multiparticle production.
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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 (December 4, 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 droplet has a stronger van der Waals interaction with the graphene surface that hampers the translational motion. We also observed a longer hydrogen bond lifetime as the density of water decreased, because the hydrophobic environment limits the libration motion of the water molecules. We also calculated the reorientational correlation time of the water molecules, and we found that the rotational motion of confined water inside the membrane is anisotropic and the reorientational correlation time of confined water is slower than that of bulk water. In addition, we employed steered molecular dynamics simulations for guiding the target molecule, and measured the free energy profile of water and ion penetration through the interstice between graphene sheets. The free energy profile of penetration revealed that the optimum interlayer distance for desalination is ~10 Å, where the minimum distance for water penetration is 7 Å. With a 7 Å interlayer distance between the graphene sheets, water molecules are stabilized inside the interlayer space because of the van der Waals interaction with the graphene sheets where sodium and chloride ions suffer from a 3–8 kcal/mol energy barrier for penetration. We believe that our simulation results would be a significant contribution for designing a new graphene-based membrane for desalination.
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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 (June 2007): 225–37. http://dx.doi.org/10.1142/s012915640700445x.
Full textAbstract:
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 and the associated THz signature was derived theoretically. The tRNA that binds amino acid tyrosine (tRNAtyr) was studied. Here, the molecular structure was optimized using the potential energy minimization and molecular dynamical (MD) simulations. Solvation effects (water molecules) were also included explicitly in the MD simulations. To verify that realistic molecular signatures were simulated, a parallel experimental study of tRNAs of E. coli was also conducted. Two very similar molecules, valine and tyrosine tRNA were investigated experimentally. Samples were prepared in the form of water solutions with the concentrations in the range 0.01-1 mg/ml. A strong correlation of the measured THz signatures associated with valine tRNA and tyrosine tRNA was observed. These findings are consistent with the structural similarity of the two tRNAs. The calculated THz signature of the tyrosine tRNA of E. coli reproduces many features of our measured spectra, and, therefore, provides valuable new insights into bio-agent detection.
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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 (May 10, 2001): 2267–91. http://dx.doi.org/10.1142/s0217751x01003457.
Full textAbstract:
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 identified. Above and below these transitions we study Mπ(T), fπ(T) and the three-space transverse and longitudinal masses [Formula: see text] and [Formula: see text]. We also study the intrinsic T-dependence of the electromagnetic coupling constant gρ(T) and the strong coupling constant gρππ(T). For both this model and a related semi-analyticinfrared dominant model, we analyze the high T behavior of the obtained masses in comparison to the M(T)→2πT behavior found in lattice QCD simulations.
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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 (June 7, 2019): 6618–31. http://dx.doi.org/10.1093/nar/gkz499.
Full textAbstract:
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 the current study can strengthen the binding affinity of ligands GR. Residue-based free energy decomposition was applied to compute ligand-nucleotide interactions and the results suggest that mutations highly affect interactions of ligands with key nucleotides U22, U51 and C74. Dynamics analyses based on MD trajectories indicate that mutations not only regulate the structural flexibility but also change the internal motion modes of GR, especially for the structures J12, J23 and J31, which implies that the aptamer domain activity of GR is extremely plastic and thus readily tunable by nucleotide mutations. This study is expected to provide useful molecular basis and dynamics information for the understanding of the function of GR and possibility as potential drug targets for antibacterial.
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Березин, К. В., К. Н. Дворецкий, М. Л. Чернавина, В. В. Нечаев, А. М. Лихтер, И. Т. Шагаутдинова, E. M. Aнтонова, and В. В. Тучин. "Оптическое просветление кожи человека in vivo рядом моносахаридов." Журнал технической физики 127, no. 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 clearing. Using complex molecular simulation of the interaction of a number of immersion clearing agents with collagen mimetic peptide (GPH)_3 using classical molecular dynamics and quantum chemistry, we found correlations between the efficiency of optical clearing and the energy of intermolecular interaction of cleaning agents with a fragment of collagen peptide.