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See detailPerturbed path integrals in imaginary time: Efficiently modeling nuclear quantum effects in molecules and materials
Poltavskyi, Igor UL; DiStasio, Robert; Tkatchenko, Alexandre UL

in Journal of Chemical Physics (2018), 148(10), 102325

Nuclear quantum effects (NQE), which include both zero-point motion and tunneling, exhibit quite an impressive range of influence over the equilibrium and dynamical properties of molecules and materials ... [more ▼]

Nuclear quantum effects (NQE), which include both zero-point motion and tunneling, exhibit quite an impressive range of influence over the equilibrium and dynamical properties of molecules and materials. In this work, we extend our recently proposed perturbed path-integral (PPI) approach for modeling NQE in molecular systems [I. Poltavsky and A. Tkatchenko, Chem. Sci. 7, 1368 (2016)], which successfully combines the advantages of thermodynamic perturbation theory with path-integral molecular dynamics (PIMD), in a number of important directions. First, we demonstrate the accuracy, performance, and general applicability of the PPI approach to both molecules and extended (condensed-phase) materials. Second, we derive a series of estimators within the PPI approach to enable calculations of structural properties such as radial distribution functions (RDFs) that exhibit rapid convergence with respect to the number of beads in the PIMD simulation. Finally, we introduce an effective nuclear temperature formalism within the framework of the PPI approach and demonstrate that such effective temperatures can be an extremely useful tool in quantitatively estimating the “quantumness” associated with different degrees of freedom in the system as well as providing a reliable quantitative assessment of the convergence of PIMD simulations. Since the PPI approach only requires the use of standard second-order imaginary-time PIMD simulations, these developments enable one to include a treatment of NQE in equilibrium thermodynamic properties (such as energies, heat capacities, and RDFs) with the accuracy of higher-order methods but at a fraction of the computational cost, thereby enabling first-principles modeling that simultaneously accounts for the quantum mechanical nature of both electrons and nuclei in large-scale molecules and materials. [less ▲]

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See detailSchNet – A deep learning architecture for molecules and materials
Schütt, Kristof T.; Sauceda, Huziel E.; Kindermans, P. J. et al

in Journal of Chemical Physics (2018), 148

Deep learning has led to a paradigm shift in artificial intelligence, including web, text, and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine ... [more ▼]

Deep learning has led to a paradigm shift in artificial intelligence, including web, text, and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine learning, in general, and deep learning, in particular, are ideally suitable for representing quantum-mechanical interactions, enabling us to model nonlinear potential-energy surfaces or enhancing the exploration of chemical compound space. Here we present the deep learning architecture SchNet that is specifically designed to model atomistic systems by making use of continuous-filter convolutional layers. We demonstrate the capabilities of SchNet by accurately predicting a range of properties across chemical space for molecules and materials, where our model learns chemically plausible embeddings of atom types across the periodic table. Finally, we employ SchNet to predict potential-energy surfaces and energy-conserving force fields for molecular dynamics simulations of small molecules and perform an exemplary study on the quantum-mechanical properties of C20- fullerene that would have been infeasible with regular ab initio molecular dynamics. [less ▲]

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See detailConservation laws and work fluctuation relations in chemical reaction networks
Rao, R.; Esposito, Massimiliano UL

in Journal of Chemical Physics (2018), 149(24),

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See detailOn the non-stationary generalized Langevin Equation
Meyer, Hugues UL; Voigtmann, Thomas; Schilling, Tanja

in Journal of Chemical Physics (2017), 147(21), 214110

In molecular dynamics simulations and single molecule experiments, observables are usually measured along dynamic trajectories and then averaged over an ensemble (“bundle”) of trajectories. Under ... [more ▼]

In molecular dynamics simulations and single molecule experiments, observables are usually measured along dynamic trajectories and then averaged over an ensemble (“bundle”) of trajectories. Under stationary conditions, the time-evolution of such averages is described by the generalized Langevin equation. By contrast, if the dynamics is not stationary, it is not a priori clear which form the equation of motion for an averaged observable has. We employ the formalism of time-dependent projection operator techniques to derive the equation of motion for a non-equilibrium trajectory-averaged observable as well as for its non-stationary auto-correlation function. The equation is similar in structure to the generalized Langevin equation but exhibits a time-dependent memory kernel as well as a fluctuating force that implicitly depends on the initial conditions of the process. We also derive a relation between this memory kernel and the autocorrelation function of the fluctuating force that has a structure similar to a fluctuation-dissipation relation. In addition, we show how the choice of the projection operator allows us to relate the Taylor expansion of the memory kernel to data that are accessible in MD simulations and experiments, thus allowing us to construct the equation of motion. As a numerical example, the procedure is applied to Brownian motion initialized in non-equilibrium conditions and is shown to be consistent with direct measurements from simulations. [less ▲]

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See detailProperties of the water to boron nitride interaction: from zero to two dimensions with benchmark accuracy
Al-Hamdani, Yasmine UL; Rossi, Mariana; Alfè, Dario et al

in Journal of Chemical Physics (2017), 147

Molecular adsorption on surfaces plays an important part in catalysis, corrosion, desalination, and various other processes that are relevant to industry and in nature. As a complement to experiments ... [more ▼]

Molecular adsorption on surfaces plays an important part in catalysis, corrosion, desalination, and various other processes that are relevant to industry and in nature. As a complement to experiments, accurate adsorption energies can be obtained using various sophisticated electronic structure methods that can now be applied to periodic systems. The adsorption energy of water on boron nitride substrates, going from zero to 2-dimensional periodicity, is particularly interesting as it calls for an accurate treatment of polarizable electrostatics and dispersion interactions, as well as posing a practical challenge to experiments and electronic structure methods. Here, we present reference adsorption energies, static polarizabilities, and dynamic polarizabilities, for water on BN substrates of varying size and dimension. Adsorption energies are computed with coupled cluster theory, fixed-node quantum Monte Carlo (FNQMC), the random phase approximation, and second order Møller-Plesset theory. These wavefunction based correlated methods are found to agree in molecular as well as periodic systems. The best estimate of the water/h-BN adsorption energy is −107 ± 7 meV from FNQMC. In addition, the water adsorption energy on the BN substrates could be expected to grow monotonically with the size of the substrate due to increased dispersion interactions, but interestingly, this is not the case here. This peculiar finding is explained using the static polarizabilities and molecular dispersion coefficients of the systems, as computed from time-dependent density functional theory (DFT). Dynamic as well as static polarizabilities are found to be highly anisotropic in these systems. In addition, the many-body dispersion method in DFT emerges as a particularly useful estimation of finite size effects for other expensive, many-body wavefunction based methods. [less ▲]

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See detailMonolayers of hard rods on planar substrates. II. Growth
Klopotek, Miriam; Hansen-Goos, Hendrik; Dixit, Mohit UL et al

in Journal of Chemical Physics (2017), 146

Growth of hard-rod monolayers via deposition is studied in a lattice model using rods with discrete orientations and in a continuum model with hard spherocylinders. The lattice model is treated with ... [more ▼]

Growth of hard-rod monolayers via deposition is studied in a lattice model using rods with discrete orientations and in a continuum model with hard spherocylinders. The lattice model is treated with kinetic Monte Carlo simulations and dynamic density functional theory while the continuum model is studied by dynamic Monte Carlo simulations equivalent to diffusive dynamics. The evolution of nematic order (excess of upright particles, “standing-up” transition) is an entropic effect and is mainly governed by the equilibrium solution, rendering a continuous transition [Paper I, M. Oettel et al., J. Chem. Phys. 145, 074902 (2016)]. Strong non-equilibrium effects (e.g., a noticeable dependence on the ratio of rates for translational and rotational moves) are found for attractive substrate potentials favoring lying rods. Results from the lattice and the continuum models agree qualitatively if the relevant characteristic times for diffusion, relaxation of nematic order, and deposition are matched properly. Applicability of these monolayer results to multilayer growth is discussed for a continuum-model realization in three dimensions where spherocylinders are deposited continuously onto a substrate via diffusion. [less ▲]

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See detailIsotropic-nematic transition and cholesteric phases of helical Yukawa rods
Kuhnhold, Anja UL; Schilling, Tanja UL

in Journal of Chemical Physics (2016), 145(194904),

We present a Monte Carlo simulation study of helical Yukawa rods as a model for chiral liquid crystal mesogens.To simulate the cholesteric phase, we introduce a newsimulation method that uses softwalls ... [more ▼]

We present a Monte Carlo simulation study of helical Yukawa rods as a model for chiral liquid crystal mesogens.To simulate the cholesteric phase, we introduce a newsimulation method that uses softwalls and self-determined boundary conditions. We observe that the isotropic-nematic phase transition is shifted to lower volume fractions with decreasing salt concentration as well as with increasing internal pitch of the rods. For particular sets of interaction parameters, the sense of the cholesteric pitch inverts, i.e., depending on concentration, mesogens of a given handedness can produce cholesteric phases of both chiral senses. [less ▲]

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See detailMonolayers of hard rods on planar substrates: I. Equilibrium
Oettel, Martin; Klopotek, Miriam; Dixit, Mohit UL et al

in Journal of Chemical Physics (2016), 145

The equilibrium properties of hard rod monolayers are investigated in a lattice model (where position and orientation of a rod are restricted to discrete values) as well as in an off-lattice model ... [more ▼]

The equilibrium properties of hard rod monolayers are investigated in a lattice model (where position and orientation of a rod are restricted to discrete values) as well as in an off-lattice model featuring spherocylinders with continuous positional and orientational degrees of freedom. Both models are treated using density functional theory and Monte Carlo simulations. Upon increasing the density of rods in the monolayer, there is a continuous ordering of the rods along the monolayer normal (“standing up” transition). The continuous transition also persists in the case of an external potential which favors flat-lying rods in the monolayer. This behavior is found in both the lattice and the continuum models. For the lattice model, we find very good agreement between the results from the specific DFT used (lattice fundamental measure theory) and simulations. The properties of lattice fundamental measure theory are further illustrated by the phase diagrams of bulk hard rods in two and three dimensions. [less ▲]

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See detailStructure diagram of binary Lennard-Jones clusters
Mravlak, Marko UL; Kister, Thomas; Kraus, Tobias et al

in Journal of Chemical Physics (2016), 145(024302),

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and ... [more ▼]

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and present a publicly accessible database of 180 000 minimal energy structures (http://softmattertheory. lu/clusters.html). We identify a variety of structures such as core-shell clusters, Janus clusters, and clusters in which the minority species is located at the vertices of icosahedra. Such clusters can be synthesized from nanoparticles in agglomeration experiments and used as building blocks in colloidal molecules or crystals. We discuss the factors that determine the formation of clusters with specific structures. [less ▲]

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See detailTransform-limited-pulse representation of excitation with natural incoherent light
Chenu, Aurélia UL; Brumer, Paul

in Journal of Chemical Physics (2016)

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See detailThe early crystal nucleation process in hard spheres shows synchronised ordering and densification
Berryman, Josh UL; Anwar, Muhammad UL; Dorosz, Sven UL et al

in Journal of Chemical Physics (2016), 145

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the ... [more ▼]

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the overcompressed liquid, beginning approximately one diffusion time before the appearance of the first “solid-like” particle of the nucleating cluster, and that a collective influx of particles towards the nucleation site occurs simultaneously to the ordering process: the density increases leading to nucleation are generated by the same individual particle displacements as the increases in order. We rule out the presence of qualitative differences in the early nucleation process between medium and low overcompressions and also provide evidence against any separation of translational and orientational order on the relevant lengthscales. [less ▲]

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See detailCommunication: Many-body stabilization of non-covalent interactions: Structure, stability, and mechanics of Ag3Co(CN)6 framework
Liu, Xiaofei; Hermann, Jan; Tkatchenko, Alexandre UL

in Journal of Chemical Physics (2016), 145(24), 241101

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See detailGlucans monomer-exchange dynamics as an open chemical network
Rao, Riccardo UL; Lacoste, David; Esposito, Massimiliano UL

in Journal of Chemical Physics (2015), 143

We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming ... [more ▼]

We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them. [less ▲]

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See detailRelaxations in the metastable rotator phase of n-eicosane
Di Giambattista, Carlo UL; Sanctuary, Roland UL; Perigo, Elio Alberto UL et al

in Journal of Chemical Physics (2015), 143

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See detailPercolation in suspensions of polydisperse hard rods: Quasi universality and finite-size effects
Meyer, Hugues UL; Van der Schoot, Paul; Schilling, Tanja UL

in Journal of Chemical Physics (2015), 143(4), 044901

We present a study of connectivity percolation in suspensions of hard spherocylinders by means of Monte Carlo simulation and connectedness percolation theory. We focus attention on polydispersity in the ... [more ▼]

We present a study of connectivity percolation in suspensions of hard spherocylinders by means of Monte Carlo simulation and connectedness percolation theory. We focus attention on polydispersity in the length, the diameter, and the connectedness criterion, and we invoke bimodal, Gaussian, and Weibull distributions for these. The main finding from our simulations is that the percolation threshold shows quasi universal behaviour, i.e., to a good approximation, it depends only on certain cumulants of the full size and connectivity distribution. Our connectedness percolation theory hinges on a Lee-Parsons type of closure recently put forward that improves upon the often-used second virial approximation [T. Schilling, M. Miller, and P. van der Schoot, e-print arXiv:1505.07660 (2015)]. The theory predicts exact universality. Theory and simulation agree quantitatively for aspect ratios in excess of 20, if we include the connectivity range in our definition of the aspect ratio of the particles. We further discuss the mechanism of cluster growth that, remarkably, differs between systems that are polydisperse in length and in width, and exhibits non-universal aspects. [less ▲]

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See detailDissipation in noisy chemical networks: The role of deficiency
Esposito, Massimiliano UL; Polettini, Matteo UL; Wachtel, Artur UL

in Journal of Chemical Physics (2015), 145(18), 184103

We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known ... [more ▼]

We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of complex behavior such as multistability and oscillations, is shown to also characterize the entropic balance. In particular, when deficiency is zero the average stochastic dissipation rate equals that of the corresponding deterministic model, where correlations are disregarded. In fact, dissipation can be reduced by the effect of noise, as occurs in a toy model of metabolism that we employ to illustrate our findings. This phenomenon highlights that there is a close interplay between deficiency and the activation of new dissipative pathways at low molecule numbers [less ▲]

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See detailThermodynamics of the polaron master equation at finite bias
Krause, T.; Brandes, T.; Esposito, Massimiliano UL et al

in Journal of Chemical Physics (2015), 142(13),

We study coherent transport through a double quantum dot. Its two electronic leads induce electronic matter and energy transport and a phonon reservoir contributes further energy exchanges. By treating ... [more ▼]

We study coherent transport through a double quantum dot. Its two electronic leads induce electronic matter and energy transport and a phonon reservoir contributes further energy exchanges. By treating the system-lead couplings perturbatively, whereas the coupling to vibrations is treated non-perturbatively in a polaron-transformed frame, we derive a thermodynamic consistent low-dimensional master equation. When the number of phonon modes is finite, a Markovian description is only possible when these couple symmetrically to both quantum dots. For a continuum of phonon modes however, also asymmetric couplings can be described with a Markovian master equation. We compute the electronic current and dephasing rate. The electronic current enables transport spectroscopy of the phonon frequency and displays signatures of Franck-Condon blockade. For infinite external bias but finite tunneling bandwidths, we find oscillations in the current as a function of the internal bias due to the electron-phonon coupling. Furthermore, we derive the full fluctuation theorem and show its identity to the entropy production in the system. (C) 2015 AIP Publishing LLC. [less ▲]

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See detailMany-body dispersion effects in the binding of adsorbates on metal surfaces
Maurer, Reinhard J.; Ruiz, Victor G.; Tkatchenko, Alexandre UL

in JOURNAL OF CHEMICAL PHYSICS (2015), 143(10),

A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we ... [more ▼]

A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we demonstrate the importance of collective van der Waals dispersion effects beyond the pairwise approximation for organic-inorganic systems on the example of atoms, molecules, and nanostructures adsorbed on metals. We use the recently developed many-body dispersion (MBD) approach in the context of density-functional theory [Tkatchenko et al., Phys. Rev. Lett. 108 236402 (2012) and Ambrosetti et al., J. Chem. Phys. 140, 18A508 (2014)] and assess its ability to correctly describe the binding of adsorbates on metal surfaces. We briefly review the MBD method and highlight its similarities to quantum-chemical approaches to electron correlation in a quasiparticle picture. In particular, we study the binding properties of xenon, 3,4,9,10-perylene-tetracarboxylic acid, and a graphene sheet adsorbed on the Ag(111) surface. Accounting for MBD effects, we are able to describe changes in the anisotropic polarizability tensor, improve the description of adsorbate vibrations, and correctly capture the adsorbate-surface interaction screening. Comparison to other methods and experiment reveals that inclusion of MBD effects improves adsorption energies and geometries, by reducing the overbinding typically found in pairwise additive dispersion-correction approaches. (C) 2015 AIP Publishing LLC. [less ▲]

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See detailCrystal growth from a supersaturated melt: Relaxation of the solid-liquid dynamic stiffness
Turci, Francesco UL; Schilling, Tanja UL

in Journal of Chemical Physics (2014), 141

We discuss the growth process of a crystalline phase out of a metastable over-compressed liquid that is brought into contact with a crystalline substrate. The process is modeled by means of molecular ... [more ▼]

We discuss the growth process of a crystalline phase out of a metastable over-compressed liquid that is brought into contact with a crystalline substrate. The process is modeled by means of molecular dynamics. The particles interact via the Lennard-Jones potential and their motion is locally thermalized by Langevin dynamics. We characterize the relaxation process of the solid-liquid interface, showing that the growth speed is maximal for liquid densities above the solid coexistence density, and that the structural properties of the interface rapidly converge to equilibrium-like properties. In particular, we show that the off-equilibrium dynamic stiffness can be extracted using capillary wave theory arguments, even if the growth front moves fast compared to the typical diffusion time of the compressed liquid, and that the dynamic stiffness converges to the equilibrium stiffness in times much shorter than the diffusion time. [less ▲]

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See detailIrreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws
Polettini, Matteo UL; Esposito, Massimiliano UL

in Journal of Chemical Physics (2014), 141

chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is ... [more ▼]

chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = sY between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats sY. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg’s theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction. [less ▲]

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