References of "Rossi, Mariana"
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See detaili-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations
Kapil, Venkat; Rossi, Mariana; Marsalek, Ondrej et al

in Computer Physics Communications (2018)

Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by ... [more ▼]

Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives. [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 detailRole of methyl-induced polarization in ion binding
Rossi, Mariana; Tkatchenko, Alexandre UL; Rempe, Susan B. et al

in Proceedings of the National Academy of Sciences of the United States of America (2013), 110(32), 12978-12983

The chemical property of methyl groups that renders them indispensable to biomolecules is their hydrophobicity. Quantum mechanical studies undertaken here to understand the effect of point substitutions ... [more ▼]

The chemical property of methyl groups that renders them indispensable to biomolecules is their hydrophobicity. Quantum mechanical studies undertaken here to understand the effect of point substitutions on potassium (K-) channels illustrate quantitatively how methyl-induced polarization also contributes to biomolecular function. K- channels regulate transmembrane salt concentration gradients by transporting K+ ions selectively. One of the K+ binding sites in the channel's selectivity filter, the S4 site, also binds Ba2+ ions, which blocks K+ transport. This inhibitory property of Ba2+ ions has been vital in understanding K-channel mechanism. In most K-channels, the S4 site is composed of four threonine amino acids. The K channels that carry serine instead of threonine are significantly less susceptible to Ba2+ block and have reduced stabilities. We find that these differences can be explained by the lower polarizability of serine compared with threonine because serine carries one less branched methyl group than threonine. A T -> S substitution in the S4 site reduces its polarizability, which, in turn, reduces ion binding by several kilocalories per mole. Although the loss in binding affinity is high for Ba2+, the loss in K+ binding affinity is also significant thermodynamically, which reduces channel stability. These results highlight, in general, how biomolecular function can rely on the polarization induced by methyl groups especially those that are proximal to charged moieties, including ions titratable amino acids, sulfates, phosphates, and nucleotides. [less ▲]

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See detailDispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals
Marom, Noa; Tkatchenko, Alexandre UL; Rossi, Mariana et al

in JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011), 7(12), 3944-3951

We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient ... [more ▼]

We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient-approximation (meta-GGA)-based functionals. This is achieved by employing conventional (semi)local and (screened-)hybrid functionals, as well as semiempirical hybrid and nonhybrid meta-GGA functionals of the M06 family, with and without interatomic pairwise Tkatchenko Scheffler corrections. All of those are tested against the benchmark S22 set of weakly bound systems a representative larger molecular complex (dimer of NiPc molecules), and a representative dispersively bound solid (hexagonal boron nitride). For the 522 database, we also compare our results with those obtained from the pairwise correction of Grimme (DFT-D3) and nonlocal Langreth Lundqvist furtctionals (vdW-DF1 and vdW-DF2). We find that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonlocal correlation needed to describe dispersion. However, long-range contributions are still missing. Pair-wise interatomic corrections, applied to conventional semilocal or hybrid functionals, or to M06 functionals, provide for a satisfactory level of accuracy irrespectively of the underlying functional. Specifically, screened-hybrid functionals such as the.Heyd Scuseria Ernzerhof (HSE) approach reduce self-interaction errors in systems possessing both localized and delocalized orbitals and can be applied to both finite and extended systems. Therefore, they serve as a useful underlying functional for dispersion corrections. [less ▲]

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