| 1. |
- Mamontov, Eugen, 1955
(author)
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Ordinary differential equation system for population of individuals and the corresponding probabilistic model
- 2008
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In: Mathl. Computer Modelling. - : Elsevier BV. - 0895-7177.
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Journal article (peer-reviewed)abstract
- The key model for particle populations in statistical mechanics is the Bogolyubov–Born– Green–Kirkwood–Yvon (BBGKY) equation chain. It is derived mainly from the Hamilton ordinary differential equation (ODE) system for the vectors of the particle states in the particle position-momentum phase space. Many problems beyond physics or chemistry, for instance, in the living-matter sciences (biology, medicine, ecology, and scoiology) make it necessary to extend the notion of a particle to an individual, or active particle. This challenge is met by the generalized kinetic theory. It implements the extension by extending the phase space from the space of the position-momentum vectors to more rich spaces formed by the state vectors with the entries which need not be limited to the entries of the position and momentum: they include other scalar variables (e.g., those associated with modelling homeorhesis or other features inherent to the individuals). One can assume that the dynamics of the state vector in the extended space, i.e. the states of the individuals (rather than common particles) is also described by an ODE system. The latter, however, need not be the Hamilton one. The question is how one can derive the analogue of the BBGKY paradigm for the new settings. The present work proposes an answer to this question. It applies a very limited number of carefully selected tools of probability theory and common statistical mechanics. It in particular uses the well-known feature that the maximum number of the individuals which can mutually interact simultaneously is bounded by a fixed value of a few units. The present approach results in the finite system of equations for the reduced many-individual distribution functions thereby eliminating the so-called closure problem inevitable in the BBGKY theory. The thermodynamic-limit assumption is not needed either. The system includes consistently derived terms of all of the basic types known in kinetic theory, in particular, both the “mean-field” and scattering-integral terms, and admits the kinetic equation of the form allowing a direct chemical-reaction reading. The present approach can deal with Hamilton’s equation systems which are nonmonogenic and not treated in statistical mechanics. The proposed modelling suggests the basis of the generalized kinetic theory and may serve as the stochastic mechanics of population of individuals.
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| 2. |
- Jiao, Yang, 1985, et al.
(author)
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Signatures of van der Waals binding: A coupling-constant scaling analysis
- 2018
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In: Physical Review B. - 2469-9969 .- 2469-9950. ; 97:8
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Journal article (peer-reviewed)abstract
- The van der Waals (vdW) density functional (vdW-DF) method [Rep. Prog. Phys. 78, 066501 (2015)RPPHAG0034-488510.1088/0034-4885/78/6/066501] describes dispersion or vdW binding by tracking the effects of an electrodynamic coupling among pairs of electrons and their associated exchange-correlation holes. This is done in a nonlocal-correlation energy term Ecnl, which permits density functional theory calculation in the Kohn-Sham scheme. However, to map the nature of vdW forces in a fully interacting materials system, it is necessary to also account for associated kinetic-correlation energy effects. Here, we present a coupling-constant scaling analysis, which permits us to compute the kinetic-correlation energy Tcnl that is specific to the vdW-DF account of nonlocal correlations. We thus provide a more complete spatially resolved analysis of the electrodynamical-coupling nature of nonlocal-correlation binding, including vdW attraction, in both covalently and noncovalently bonded systems. We find that kinetic-correlation energy effects play a significant role in the account of vdW or dispersion interactions among molecules. Furthermore, our mapping shows that the total nonlocal-correlation binding is concentrated to pockets in the sparse electron distribution located between the material fragments.
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| 3. |
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| 4. |
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| 5. |
- Baggioli, Matteo, et al.
(author)
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Holographic plasmon relaxation with and without broken translations
- 2019
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In: Journal of High Energy Physics (JHEP). - : SPRINGER. - 1126-6708 .- 1029-8479. ; :9
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Journal article (peer-reviewed)abstract
- We study the dynamics and the relaxation of bulk plasmons in strongly coupled and quantum critical systems using the holographic framework. We analyze the dispersion relation of the plasmonic modes in detail for an illustrative class of holographic bottom-up models. Comparing to a simple hydrodynamic formula, we entangle the complicated interplay between the three least damped modes and shed light on the underlying physical processes. Such as the dependence of the plasma frequency and the effective relaxation time in terms of the electromagnetic coupling, the charge and the temperature of the system. Introducing momentum dissipation, we then identify its additional contribution to the damping. Finally, we consider the spontaneous symmetry breaking (SSB) of translational invariance. Upon dialing the strength of the SSB, we observe an increase of the longitudinal sound speed controlled by the elastic moduli and a decrease in the plasma frequency of the gapped plasmon. We comment on the condensed matter interpretation of this mechanism.
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| 6. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(author)
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Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
- 2015
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In: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878
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Journal article (peer-reviewed)abstract
- Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
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| 7. |
- Erhart, Paul, 1978
(author)
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A first-principles study of helium storage in oxides and at oxide-iron interfaces
- 2012
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In: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 111:11
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Journal article (peer-reviewed)abstract
- Density-functional theory calculations based on conventional as well as hybrid exchange-correlation functionals have been carried out to study the properties of helium in various oxides (Al2O3, TiO2, Y2O3, YAP, YAG, YAM, MgO, CaO, BaO, SrO) as well as at oxide-iron interfaces. Helium interstitials in bulk oxides are shown to be energetically more favorable than substitutional helium, yet helium binds to existing vacancies. The solubility of He in oxides is systematically higher than in iron and scales with the free volume at the interstitial site nearly independently of the chemical composition of the oxide. In most oxides, He migration is significantly slower and He-He binding is much weaker than in iron. To quantify the solubility of helium at oxide-iron interfaces two prototypical systems are considered (Fe-MgO, Fe-FeO-MgO). In both cases, the He solubility is markedly enhanced in the interface compared to either of the bulk phases. The results of the calculations allow to construct a schematic energy landscape for He interstitials in iron. The implications of these results are discussed in the context of helium sequestration in oxide dispersion strengthened steels, including the effects of interfaces and lattice strain.
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| 8. |
- Hellsvik, Johan, et al.
(author)
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General method for atomistic spin-lattice dynamics with first-principles accuracy
- 2019
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In: Physical Review B. - : American Physical Society. - 2469-9969 .- 2469-9950. ; 99:10
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Journal article (peer-reviewed)abstract
- We present a computationally efficient and general first-principles based method for spin-lattice simulations for solids and clusters. The method is based on a coupling of atomistic spin dynamics and molecular dynamics simulations, expressed through a spin-lattice Hamiltonian, where the bilinear magnetic term is expanded up to second order in displacement. The effect of first-order spin-lattice coupling on the magnon and phonon dispersion in bcc Fe is reported as an example, and we observe good agreement with previous simulations. We also illustrate the coupled spin-lattice dynamics method on a more conceptual level, by exploring dissipation-free spin and lattice motion of small magnetic clusters (a dimer, trimer, and tetramer). The method discussed here opens the door for a quantitative description and understanding of the microscopic origin of many fundamental phenomena of contemporary interest, such as ultrafast demagnetization, magnetocalorics, and spincaloritronics.
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| 9. |
- Noble, Charleston, et al.
(author)
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A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.
- 2015
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:4
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Journal article (peer-reviewed)abstract
- Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA.
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| 10. |
- Catena, Riccardo, 1978, et al.
(author)
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Dark matter-electron interactions in materials beyond the dark photon model
- 2023
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In: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; 2023:3
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Journal article (peer-reviewed)abstract
- The search for sub-GeV dark matter (DM) particles via electronic transitions in underground detectors attracted much theoretical and experimental interest in the past few years. A still open question in this field is whether experimental results can in general be interpreted in a framework where the response of detector materials to an external DM probe is described by a single ionisation or crystal form factor, as expected for the so-called dark photon model. Here, ionisation and crystal form factors are examples of material response functions: interaction-specific integrals of the initial and final state electron wave functions. In this work, we address this question through a systematic classification of the material response functions induced by a wide range of models for spin-0, spin-1/2 and spin-1 DM. We find several examples for which an accurate description of the electronic transition rate at DM direct detection experiments requires material response functions that go beyond those expected for the dark photon model. This concretely illustrates the limitations of a framework that is entirely based on the standard ionisation and crystal form factors, and points towards the need for the general response-function-based formalism we pushed forward recently [1,2]. For the models that require non-standard atomic and crystal response functions, we use the response functions of [1,2] to calculate the DM-induced electronic transition rate in atomic and crystal detectors, and to present 90% confidence level exclusion limits on the strength of the DM-electron interaction from the null results reported by XENON10, XENON1T, EDELWEISS and SENSEI.
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