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Performance of various density-functional approximations for cohesive properties of 64 bulk solids ; ; Tkatchenko, Alexandre et al in New Journal of Physics (2018), 20 Accurate and careful benchmarking of different density-functional approximations (DFAs) represents an important source of information for understanding DFAs and how to improve them. In this work we have ... [more ▼] Accurate and careful benchmarking of different density-functional approximations (DFAs) represents an important source of information for understanding DFAs and how to improve them. In this work we have studied the lattice constants, cohesive energies, and bulk moduli of 64 solids using six functionals, representing the local, semi-local, and hybrid DFAs on the first four rungs of Jacob’s ladder. The set of solids considered consists of ionic crystals, semiconductors, metals, and transition metal carbides and nitrides. To minimize numerical errors and to avoid making further approximations, the full-potential, all-electron FHI-aims code has been employed, and all the reported cohesive properties include contributions from zero-point vibrations. Our assessment demonstrates that current DFAs can predict cohesive properties with mean absolute relative errors of 0.6% for the lattice constant and6%for both the cohesive energy and the bulk modulus over the whole database of 64 solids. For semiconducting and insulating solids, the recently proposed SCAN meta-GGA functional represents a substantial improvement over the other functionals. However, when considering the different types of solids in the set, all of the employed functionals exhibit some variance in their performance. There are clear trends and relationships in the deviations of the cohesive properties, pointing to the need to consider, for example, long-range van der Waals (vdW) interactions. This point is also demonstrated by consistent improvements in predictions for cohesive properties of semiconductors when augmentingGGAand hybrid functionals with a screened Tkatchenko– Scheffler vdW energy term. [less ▲] Detailed reference viewed: 100 (0 UL)Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten Wachtel, Artur ; Rao, Riccardo ; Esposito, Massimiliano in New Journal of Physics (2018), 20(4), 042002 Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries ... [more ▼] Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Our results lay the foundations for systematic studies of the thermodynamics of large-scale biochemical reaction networks. Moreover, we identify the conditions under which a relation between one-way fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux–force relation. As a further consequence we show that, in contrast to common belief, the second law of thermodynamics does not require the currents and the forces of biochemical reaction networks to be always aligned. [less ▲] Detailed reference viewed: 152 (4 UL)Conservation Laws Shape Dissipation Rao, Riccardo ; Esposito, Massimiliano in New Journal of Physics (2018), 20 Starting from the most general formulation of stochastic thermodynamics—i.e. a thermodynamically consistent nonautonomous stochastic dynamics describing systems in contact with several reservoirs —we ... [more ▼] Starting from the most general formulation of stochastic thermodynamics—i.e. a thermodynamically consistent nonautonomous stochastic dynamics describing systems in contact with several reservoirs —we define a procedure to identify the conservative and the minimal set of nonconservative contributions in the entropy production. The former is expressed as the difference between changes caused by time-dependent drivings and a generalized potential difference. The latter is a sum over the minimal set of flux-force contributions controlling the dissipative flows across the system. When the system is initially prepared at equilibrium (e.g. by turning off drivings and forces), a finite-time detailed fluctuation theorem holds for the different contributions. Our approach relies on identifying the complete set of conserved quantities and can be viewed as the extension of the theory of generalized Gibbs ensembles to nonequilibrium situations. [less ▲] Detailed reference viewed: 126 (7 UL)In-phase and anti-phase flagellar synchronization by waveform compliance and basal coupling ; ; Wagner, Christian et al in New Journal of Physics (2017) Cilia and flagella exhibit regular bending waves that perform mechanical work on the surrounding fluid, to propel cellular swimmers and pump fluids inside organisms. Here, we quantify a force-velocity ... [more ▼] Cilia and flagella exhibit regular bending waves that perform mechanical work on the surrounding fluid, to propel cellular swimmers and pump fluids inside organisms. Here, we quantify a force-velocity relationship of the beating flagellum, by exposing flagellated Chlamydomonas cells to controlled microfluidic flows. A simple theory of flagellar limit-cycle oscillations, calibrated by measurements in the absence of flow, reproduces this relationship quantitatively. We derive a link between the energy efficiency of the flagellar beat and its ability to synchronize to oscillatory flows. [less ▲] Detailed reference viewed: 35 (1 UL)Stochastic thermodynamics of rapidly driven quantum systems, Bulnes Cuetara, Gregory ; ; Esposito, Massimiliano in New Journal of Physics (2015), 17 We present the stochastic thermodynamics analysis of an open quantum system weakly coupled to multiple reservoirs and driven by a rapidly oscillating external field. The analysis is built on a modified ... [more ▼] We present the stochastic thermodynamics analysis of an open quantum system weakly coupled to multiple reservoirs and driven by a rapidly oscillating external field. The analysis is built on a modified stochastic master equation in the Floquet basis. Transition rates are shown to satisfy the local detailed balance involving the entropy flowing out of the reservoirs. The first and second law of thermodynamics are also identified at the trajectory level. Mechanical work is identified by means of initial and final projections on energy eigenstates of the system. We explicitly show that this two step measurement becomes unnecessary in the long time limit. A steady-state fluctuation theorem for the currents and rate of mechanical work is also established. This relation does not require the introduction of a time reversed external driving which is usually needed when considering systems subjected to time asymmetric external fields. This is understood as a consequence of the secular approximation applied in consistency with the large time scale separation between the fast driving oscillations and the slower relaxation dynamics induced by the environment. Our results are finally illustrated on a model describing a thermodynamic engine. [less ▲] Detailed reference viewed: 156 (11 UL)Double quantum dot coupled to a quantum point contact: A stochastic thermodynamics approach ; Esposito, Massimiliano in New Journal of Physics (2015), 17(9), We study the nonequilibrium properties of an electronic circuit composed of a double quantum dot (DQD) channel capacitively coupled to a quantum point contact (QPC) within the framework of stochastic ... [more ▼] We study the nonequilibrium properties of an electronic circuit composed of a double quantum dot (DQD) channel capacitively coupled to a quantum point contact (QPC) within the framework of stochastic thermodynamics. We show that the transition rates describing the dynamics satisfy a nontrivial local detailed balance and that the statistics of energy and particle currents across both channels obeys a fluctuation theorem. We analyze two regimes where the device operates as a thermodynamic machine and study its output power and efficiency fluctuations. We show that the electrons tunneling through the QPC without interacting with the DQD have a strong effect on the device efficiency. © 2015 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft. [less ▲] Detailed reference viewed: 128 (4 UL)Kinetics and thermodynamics of reversible polymerization in closed systems ; ; Esposito, Massimiliano et al in New Journal of Physics (2015), 17(8), Motivated by a recent study on the metabolism of carbohydrates in bacteria, we study the kinetics and thermodynamics of two classic models for reversible polymerization, one preserving the total polymer ... [more ▼] Motivated by a recent study on the metabolism of carbohydrates in bacteria, we study the kinetics and thermodynamics of two classic models for reversible polymerization, one preserving the total polymer concentration and the other one not. The chemical kinetics is described by rate equations following the mass-action law. We consider a closed system and nonequilibrium initial conditions and show that the system dynamically evolves towards equilibrium where a detailed balance is satisfied. The entropy production during this process can be expressed as the time derivative of a Lyapunov function. When the solvent is not included in the description and the dynamics conserves the total concentration of polymer, the Lyapunov function can be expressed as a Kullback-Leibler divergence between the nonequilibrium and the equilibrium polymer length distribution. The same result holds true when the solvent is explicitly included in the description and the solution is assumed dilute, whether or not the total polymer concentration is conserved. Furthermore, in this case a consistent nonequilibrium thermodynamic formulation can be established and the out-of-equilibrium thermodynamic enthalpy, entropy and free energy can be identified. Such a framework is useful in complementing standard kinetics studies with the dynamical evolution of thermodynamic quantities during polymerization. © 2015 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft. [less ▲] Detailed reference viewed: 99 (4 UL)Work statistics in stochastically driven systems Verley, Gatien ; ; Esposito, Massimiliano in New Journal of Physics (2014), 16 We identify the conditions under which a stochastic driving that induces energy changes into a system coupled with a thermal bath can be treated as a work source. When these conditions are met, the work ... [more ▼] We identify the conditions under which a stochastic driving that induces energy changes into a system coupled with a thermal bath can be treated as a work source. When these conditions are met, the work statistics satisfy the Crooks fluctuation theorem traditionally derived for deterministic drivings. We illustrate this fact by calculating and comparing the work statistics for a two-level system driven respectively by a stochastic and a deterministic piecewise constant protocol. [less ▲] Detailed reference viewed: 112 (9 UL)Experimental observation of magnetic poles inside bulk magnets via q \neq 0 Fourier modes of magnetostatic field Perigo, Elio Alberto ; ; et al in New Journal of Physics (2014), 16 Detailed reference viewed: 69 (2 UL)Single-electron transistor strongly coupled to vibrations: counting statistics and fluctuation theorem ; ; et al in New Journal of Physics (2013), 033032 Using a simple quantum master equation approach, we calculate the full counting statistics of a single-electron transistor strongly coupled to vibrations. The full counting statistics contains both the ... [more ▼] Using a simple quantum master equation approach, we calculate the full counting statistics of a single-electron transistor strongly coupled to vibrations. The full counting statistics contains both the statistics of integrated particle and energy currents associated with the transferred electrons and phonons. A universal as well as an effective fluctuation theorem are derived for the general case where the various reservoir temperatures and chemical potentials are different. The first relates to the entropy production generated in the junction, while the second reveals internal information of the system. The model recovers the Franck–Condon blockade, and potential applications to noninvasive molecular spectroscopy are discussed. [less ▲] Detailed reference viewed: 86 (5 UL)Data pattern tomography: reconstruction with an unknown apparatus Ignatenko, Andrew ; ; et al in New Journal of Physics (2013), 15 We propose a scheme for the reconstruction of the quantum state without a priori knowledge about the measurement setup. Using the data pattern approach, we develop an iterative procedure for obtaining ... [more ▼] We propose a scheme for the reconstruction of the quantum state without a priori knowledge about the measurement setup. Using the data pattern approach, we develop an iterative procedure for obtaining information about the measurement which is sufficient for an estimation of a particular signal state. The method is illustrated with the examples of reconstruction with on/off detection and quantum homodyne tomography. [less ▲] Detailed reference viewed: 82 (6 UL)Machine learning of molecular electronic properties in chemical compound space ; ; et al in NEW JOURNAL OF PHYSICS (2013), 15 The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful ... [more ▼] The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy polarizability, frontier orbital eigenvalues, ionization potential electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a `quantum machine' is similar, and sometimes superior, to modern quantum-chemical methods-at negligible computational cost. [less ▲] Detailed reference viewed: 275 (1 UL)Structure and energetics of benzene adsorbed on transition-metal surfaces: density-functional theory with van der Waals interactions including collective substrate response ; ; et al in NEW JOURNAL OF PHYSICS (2013), 15 The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a ... [more ▼] The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a significant challenge for both theory and experiment. Using the Perdew-Burke-Ernzerhof (PBE), PBE+vdW (van der Waals) and the recently developed PBE+vdW(surf) (density-functional theory with vdW interactions that include the collective electronic response of the substrate) methods, we calculated the structures and energetics for benzene on transition-metal surfaces: Cu, Ag, Au, Pd, Pt, Rh and Ir. Our calculations demonstrate that vdW interactions increase the binding energy by more than 0.70 eV for physisorbed systems (Cu, Ag and Au) and by an even larger amount for strongly bound systems (Pd, Pt, Rh and Ir). The collective response of the substrate electrons captured via the vdW(surf) method plays a significant role for most substrates shortening the equilibrium distance by 0.25 angstrom for Cu and decreasing the binding energy by 0.27 eV for Rh. The reliability of our results is assessed by comparison with calculations using the random-phase approximation including renormalized single excitations and the experimental data from temperature-programmed desorption microcalorimetry measurements and low-energy electron diffraction. [less ▲] Detailed reference viewed: 126 (0 UL)Contribution of the buffer layer to the Raman spectrum of epitaxial graphene on SiC(0001) ; ; Molina-Sanchez, Alejandro et al in New Journal of Physics (2013), 15(4), 043031 We report a Raman study of the so-called buffer layer with $(6 3 6 3)R30^ $ periodicity which forms the intrinsic interface structure between epitaxial graphene and SiC(0001). We show that this interface ... [more ▼] We report a Raman study of the so-called buffer layer with $(6 3 6 3)R30^ $ periodicity which forms the intrinsic interface structure between epitaxial graphene and SiC(0001). We show that this interface structure leads to a non-vanishing signal in the Raman spectrum at frequencies in the range of the D- and G-band of graphene and discuss its shape and intensity. Ab initio phonon calculations reveal that these features can be attributed to the vibrational density of states of the buffer layer. [less ▲] Detailed reference viewed: 104 (5 UL)Resolution-of-identity approach to Hartree-Fock, hybrid density functionals, RPA, MP2 and GW with numeric atom-centered orbital basis functions ; ; et al in NEW JOURNAL OF PHYSICS (2012), 14 The efficient implementation of electronic structure methods is essential for first principles modeling of molecules and solids. We present here a particularly efficient common framework for methods ... [more ▼] The efficient implementation of electronic structure methods is essential for first principles modeling of molecules and solids. We present here a particularly efficient common framework for methods beyond semilocal density-functional theory (DFT), including Hartree-Fock (HF), hybrid density functionals, random-phase approximation (RPA) second-order Moller-Plesset perturbation theory (MP2) and the GW method. This computational framework allows us to use compact and accurate numeric atom-centered orbitals (NAOs), popular in many implementations of semilocal DFT, as basis functions. The essence of our framework is to employ the `resolution of identity (RI)' technique to facilitate the treatment of both the two-electron Coulomb repulsion integrals (required in all these approaches) and the linear density-response function (required for RPA and GW). This is possible because these quantities can be expressed in terms of the products of single-particle basis functions, which can in turn be expanded in a set of auxiliary basis functions (ABFs). The construction of ABFs lies at the heart of the RI technique, and we propose here a simple prescription for constructing ABFs which can be applied regardless of whether the underlying radial functions have a specific analytical shape (e.g. Gaussian) or are numerically tabulated. We demonstrate the accuracy of our RI implementation for Gaussian and NAO basis functions, as well as the convergence behavior of our NAO basis sets for the above-mentioned methods. Benchmark results are presented for the ionization energies of 50 selected atoms and molecules from the G2 ion test set obtained with the GW and MP2 self-energy methods, and the G2-I atomization energies as well as the S22 molecular interaction energies obtained with the RPA method. [less ▲] Detailed reference viewed: 87 (0 UL)Combination of high performance refractometry and infrared spectroscopy as a probe for chemically induced gelation and vitrification of epoxies Müller, Ulrich ; Philipp, Martine ; Gervais, P. C. et al in New Journal of Physics (2010), 12 A combination of infrared spectroscopy and high performance refractometry was used to investigate the chemically induced sol-gel and glass transition during the polymerization of epoxies. Representations ... [more ▼] A combination of infrared spectroscopy and high performance refractometry was used to investigate the chemically induced sol-gel and glass transition during the polymerization of epoxies. Representations of the refractive index versus chemical conversion reveal an interesting insight in the optical properties accompanying gelation and vitrification. Whereas the electronic polarizability of the liquid state of small average molecular mass and the glassy state is dominated by the mass density, an unexpected excess polarizability observed during the gelation is attributed to cooperative dipole-dipole interactions. [less ▲] Detailed reference viewed: 79 (1 UL)Entropy production as correlation between system and reservoir Esposito, Massimiliano ; ; in New Journal of Physics (2010), 12 We derive an exact (classical and quantum) expression for the entropy production of a finite system placed in contact with one or several finite reservoirs, each of which is initially described by a ... [more ▼] We derive an exact (classical and quantum) expression for the entropy production of a finite system placed in contact with one or several finite reservoirs, each of which is initially described by a canonical equilibrium distribution. Although the total entropy of system plus reservoirs is conserved, we show that system entropy production is always positive and is a direct measure of system–reservoir correlations and/or entanglements. Using an exactly solvable quantum model, we illustrate our novel interpretation of the Second Law in a microscopically reversible finite-size setting, with strong coupling between the system and the reservoirs. With this model, we also explicitly show the approach of our exact formulation to the standard description of irreversibility in the limit of a large reservoir. [less ▲] Detailed reference viewed: 54 (0 UL)Interphases, gelation, vitrication, porous glasses and the generalized Cauchy relation: epoxy/silica nanocomposites Philipp, Martine ; Müller, Ulrich ; et al in New Journal of Physics (2009), 11(2), 023015 The generalized Cauchy relation (gCR) of epoxy/silica nanocomposites does not show either the chemically induced sol–gel transition or the chemically induced glass transition in the course of ... [more ▼] The generalized Cauchy relation (gCR) of epoxy/silica nanocomposites does not show either the chemically induced sol–gel transition or the chemically induced glass transition in the course of polymerization. Astonishingly, by varying the silica nanoparticles’ concentration between 0 and 25 vol%in the composites, the Cauchy parameter A of the gCR remains universal and can be determined from the pure epoxy’s elastic moduli. Air-ﬁlled porous silica glasses are considered as models for percolated silica particles. A longitudinal modulus versus density representation evidences the aforementioned transition phenomena during polymerization of the epoxy/silica nanocomposites. The existence of optically and mechanically relevant interphases is discussed. [less ▲] Detailed reference viewed: 77 (1 UL)Organization versus frustration: low temperature transitions in a gelatine-based gel Philipp, Martine ; Müller, Ulrich ; Sanctuary, Roland et al in New Journal of Physics (2008), 10 A commercial physical gel composed of gelatine, water and glycerol shows a sol–gel transition which has been resolved by optical rotation measurements by step-wise heating the gel. This transition is not ... [more ▼] A commercial physical gel composed of gelatine, water and glycerol shows a sol–gel transition which has been resolved by optical rotation measurements by step-wise heating the gel. This transition is not observable in the longitudinal acoustic mode measured at hypersonic frequencies with Brillouin spectroscopy. Depending on the thermal treatment of the investigated material during the sol–gel transition and within the gel state, Brillouin spectroscopy reflects tremendously different hypersonic dynamics. These distinct dynamics are responsible for the formation of different glassy states at low temperatures including that of a glass-ceramic. The large variety of super-cooled and glassy states is attributed to distinct distributions of the gel's constituents within the samples. Surprisingly, the same gel state can be produced either by annealing the gel over months or by the non-equilibrium effect of thermo-diffusion (Soret effect) in the course of some minutes. [less ▲] Detailed reference viewed: 53 (1 UL)Acoustic Profilometry Of Interphases In An Epoxy Due To Segregation and Diffusion Using Brillouin Microscopy. Müller, Ulrich ; ; Baller, Jörg et al in New Journal of Physics (2008), 10(2), 023-031 Reactive network forming polymer systems like epoxies are of huge technological interest because of their adhesive properties based on specific interactions with a large variety of materials. These ... [more ▼] Reactive network forming polymer systems like epoxies are of huge technological interest because of their adhesive properties based on specific interactions with a large variety of materials. These specific interactions alter the morphology of the epoxy within areas determined by the correlation length of these interactions. The changed morphology leads to interphases with altered (mechanical) properties. Besides these surface-induced interphases, bulk interphases do occur due to segregation, crystallization, diffusion, etc. A new experimental technique to characterize such mechanical interphases is μ-Brillouin spectroscopy (μ-BS). With μ-BS, we studied interphases and their formation in epoxies due to segregation of the constituent components and due to selective diffusion of one component. In the latter case, we will demonstrate the influence of changing the boundary conditions of the diffusion process on the shape of the interphase. 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