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Theory of simulation

F Pelin Kinik, Cigdem Altintas, Volkan Balci, Burak Koyuturk, Alper Uzun, Seda Keskin
Experiments were combined with atomically-detailed simulations and density functional theory (DFT) calculations to understand the effect of incorporation of an ionic liquid (IL), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), into a metal organic framework (MOF with a zeolitic imidazolate framework), ZIF-8, on the CO2 separation performance. The interactions between [BMIM][PF6] and ZIF-8 were examined in deep detail and their consequences on CO2/CH4, CO2/N2, and CH4/N2 separation have been elucidated by using experimental measurements complemented by DFT calculations and atomically-detailed simulations...
October 26, 2016: ACS Applied Materials & Interfaces
M Hossein Khalilian, Saber Mirzaei, Avat Arman Taherpour
The electronic features of anti-tumor agent, temozolomide, and its degradation products (MTIC and metabolite AIC) have been traced by means of UV absorption spectroscopy in vacuo and aqueous media. For comparison, electronic spectra of related structures and drugs (e.g., dacarbazine) were also investigated. These investigations were carried out using time-dependent density functional theory (TD-DFT) method while the conductor like screening model (COSMO) were applied for the inclusion of solvent effects in electronic spectra...
November 2016: Journal of Molecular Modeling
Hiroshi Watanabe, Hajime Inaoka, Nobuyasu Ito
The ripening kinetics of bubbles is studied by performing molecular dynamics simulations. From the time evolution of a system, the growth rates of individual bubbles are determined. At low temperatures, the system exhibits a t(1/2) law and the growth rate is well described by classical Lifshitz-Slyozov-Wagner (LSW) theory for the reaction-limited case. This is direct evidence that the bubble coarsening at low temperatures is reaction-limited. At high temperatures, although the system exhibits a t(1/3) law, which suggests that it is diffusion-limited, the accuracy of the growth rate is insufficient to determine whether the form is consistent with the prediction of LSW theory for the diffusion-limited case...
September 28, 2016: Journal of Chemical Physics
Henry S Ashbaugh, Natalia da Silva Moura, Hayden Houser, Yang Wang, Amy Goodson, J Wesley Barnett
Theoretical descriptions of molecular-scale solvation frequently invoke contributions proportional to the solvent exposed area, under the tacit expectation that those contributions are tied to a surface tension for macroscopic surfaces. Here we examine the application of revised scaled-particle theory (RSPT) to extrapolate molecular simulation results for the wetting of molecular-to-meso-scale repulsive solutes in liquid water and decane to determine the interfacial free energies of hard, flat surfaces. We show that the RSPT yields interfacial free energies at ambient pressures that are consistently greater than that obtained from the liquid-vapor surface tensions of water and decane by ∼4%...
September 28, 2016: Journal of Chemical Physics
S Orioli, P Faccioli
Renormalization Group (RG) theory provides the theoretical framework to define rigorous effective theories, i.e., systematic low-resolution approximations of arbitrary microscopic models. Markov state models are shown to be rigorous effective theories for Molecular Dynamics (MD). Based on this fact, we use real space RG to vary the resolution of the stochastic model and define an algorithm for clustering microstates into macrostates. The result is a lower dimensional stochastic model which, by construction, provides the optimal coarse-grained Markovian representation of the system's relaxation kinetics...
September 28, 2016: Journal of Chemical Physics
Tonnam Balankura, Xin Qi, Ya Zhou, Kristen A Fichthorn
In the shape-controlled synthesis of colloidal Ag nanocrystals, structure-directing agents, particularly polyvinylpyrrolidone (PVP), are known to be a key additive in making nanostructures with well-defined shapes. Although many Ag nanocrystals have been successfully synthesized using PVP, the mechanism by which PVP actuates shape control remains elusive. Here, we present a multi-scale theoretical framework for kinetic Wulff shape predictions that accounts for the chemical environment, which we used to probe the kinetic influence of the adsorbed PVP film...
October 14, 2016: Journal of Chemical Physics
Russell K W Spencer, Paul F Curry, Robert A Wickham
We examine nucleation of the stable body-centred-cubic (BCC) phase from the metastable uniform disordered phase in an asymmetric diblock copolymer melt. Our comprehensive, large-scale simulations of the time-dependent, mean-field Landau-Brazovskii model find that spherical droplets of the BCC phase nucleate directly from disorder. Near the order-disorder transition, the critical nucleus is large and has a classical profile, attaining the bulk BCC phase in an interior that is separated from disorder by a sharp interface...
October 14, 2016: Journal of Chemical Physics
Simon P Neville, Vitali Averbukh, Marco Ruberti, Renjie Yun, Serguei Patchkovskii, Majed Chergui, Albert Stolow, Michael S Schuurman
We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L(2) method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian...
October 14, 2016: Journal of Chemical Physics
Max Boleininger, Anne Ay Guilbert, Andrew P Horsfield
To interpret ultrafast dynamics experiments on large molecules, computer simulation is required due to the complex response to the laser field. We present a method capable of efficiently computing the static electronic response of large systems to external electric fields. This is achieved by extending the density-functional tight binding method to include larger basis sets and by multipole expansion of the charge density into electrostatically interacting Gaussian distributions. Polarizabilities for a range of hydrocarbon molecules are computed for a multipole expansion up to quadrupole order, giving excellent agreement with experimental values, with average errors similar to those from density functional theory, but at a small fraction of the cost...
October 14, 2016: Journal of Chemical Physics
Yu Wang, Xiao Zheng, Jinlong Yang
Transition metal phthalocyanine molecules adsorbed on a metal substrate exhibit rich spin-related phenomena such as magnetic anisotropy, spin excitation, and Kondo effect. In this work, we investigate theoretically few-layer cobalt phthalocyanine (CoPc) molecular assembly stacking on Pb(111) surface with the use of a combined density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. Calculation results indicate that the local spin properties of CoPc/Pb(111) composites depend critically on the number of adsorption layers...
October 21, 2016: Journal of Chemical Physics
Jonathan M Martin, Wei Li, Kris T Delaney, Glenn H Fredrickson
We present a new molecularly informed statistical field theory model of inhomogeneous polarizable soft matter. The model is based on fluid elements, referred to as beads, that can carry a net monopole of charge at their center of mass and a fixed or induced dipole through a Drude-type distributed charge approach. The beads are thus polarizable and naturally manifest attractive van der Waals interactions. Beyond electrostatic interactions, beads can be given soft repulsions to sustain fluid phases at arbitrary densities...
October 21, 2016: Journal of Chemical Physics
Dominik Sidler, Arthur Schwaninger, Sereina Riniker
In molecular dynamics (MD) simulations, free-energy differences are often calculated using free energy perturbation or thermodynamic integration (TI) methods. However, both techniques are only suited to calculate free-energy differences between two end states. Enveloping distribution sampling (EDS) presents an attractive alternative that allows to calculate multiple free-energy differences in a single simulation. In EDS, a reference state is simulated which "envelopes" the end states. The challenge of this methodology is the determination of optimal reference-state parameters to ensure equal sampling of all end states...
October 21, 2016: Journal of Chemical Physics
Andrei Kryjevski, Brendan Gifford, Svetlana Kilina, Dmitri Kilin
Efficient multiple exciton generation (MEG) in chiral single-wall carbon nanotubes (SWCNTs) is present within the solar spectrum range as shown by the many-body perturbation theory calculations combined with the density functional theory simulations. To describe the impact ionization process, we calculate exciton-to-biexciton decay rates R1→2 and biexciton-to-exciton rates R2→1 in the (6,2) and (10,5) SWCNTs. Within the solar energy range, we predict R1→2 ∼ 10(14) s(-1), while biexciton-to-exciton recombination is weak with R2→1/R1→2 ≤ 10(-2)...
October 21, 2016: Journal of Chemical Physics
Tuan Anh Pham, Tadashi Ogitsu, Edmond Y Lau, Eric Schwegler
Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems...
October 21, 2016: Journal of Chemical Physics
Lei Liu, Cui-E Hu, Mei Tang, Xiang-Rong Chen, Ling-Cang Cai
The low-lying isomers of cationic water cluster (H2O)6(+) have been globally explored by using particle swarm optimization algorithm in conjunction with quantum chemical calculations. Compared with previous results, our searching method covers a wide range of structural isomers of (H2O)6(+) and therefore turns out to be more effective. With these local minima, geometry optimization and vibrational analysis are performed for the most interesting clusters at second-order Møller-Plesset (MP2)/aug-cc-pVDZ level, and their energies are further refined at MP2/aug-cc-pVTZ and coupled-cluster theory with single, double, and perturbative triple excitations/aug-cc-pVDZ level...
October 21, 2016: Journal of Chemical Physics
Saman Alavi, Ryo Ohmura
When compressed with water or ice under high pressure and low temperature conditions, some gases form solid gas hydrate inclusion compounds which have higher melting points than ice under those pressures. In this work, we study the balance of the guest-water and water-water interaction energies that lead to the formation of the clathrate hydrate phases. In particular, molecular dynamics simulations with accurate water potentials are used to study the energetics of the formation of structure I (sI) and II (sII) clathrate hydrates of methane, ethane, and propane...
October 21, 2016: Journal of Chemical Physics
Amartya S Banerjee, Lin Lin, Wei Hu, Chao Yang, John E Pask
The Discontinuous Galerkin (DG) electronic structure method employs an adaptive local basis (ALB) set to solve the Kohn-Sham equations of density functional theory in a discontinuous Galerkin framework. The adaptive local basis is generated on-the-fly to capture the local material physics and can systematically attain chemical accuracy with only a few tens of degrees of freedom per atom. A central issue for large-scale calculations, however, is the computation of the electron density (and subsequently, ground state properties) from the discretized Hamiltonian in an efficient and scalable manner...
October 21, 2016: Journal of Chemical Physics
Shane M Parker, Saswata Roy, Filipp Furche
Transition densities between excited states are key for nonlinear theoretical spectroscopy and multi-state non-adiabatic molecular dynamics (NAMD) simulations. In the framework of response theory, these transition densities are accessible from poles of the quadratic response function. It was shown recently that the thus obtained transition densities within time-dependent Hartree-Fock (TDHF) and adiabatic time-dependent density functional theory (TDDFT) exhibit unphysical divergences when the difference in excitation energy of the two states of interest matches another excitation energy...
October 7, 2016: Journal of Chemical Physics
Brian K Radak, Benoît Roux
Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory...
October 7, 2016: Journal of Chemical Physics
Anh Nguyen Duc, Marcel Wolbers
Composite endpoints are widely used as primary endpoints of randomized controlled trials across clinical disciplines. A common critique of the conventional analysis of composite endpoints is that all disease events are weighted equally, whereas their clinical relevance may differ substantially. We address this by introducing a framework for the weighted analysis of composite endpoints and interpretable test statistics, which are applicable to both binary and time-to-event data. To cope with the difficulty of selecting an exact set of weights, we propose a method for constructing simultaneous confidence intervals and tests that asymptotically preserve the family-wise type I error in the strong sense across families of weights satisfying flexible inequality or order constraints based on the theory of χ¯2-distributions...
October 26, 2016: Statistics in Medicine
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