All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome.

The spliceosome (SPL) is a majestic macromolecular machinery composed of five small nuclear RNAs and hundreds of proteins. SPL removes noncoding introns from precursor messenger RNAs (pre-mRNAs) and ligates coding exons, giving rise to functional mRNAs. Building on the first SPL structure solved at near-atomic-level resolution, here we elucidate the functional dynamics of the intron lariat spliceosome (ILS) complex through multi-microsecond-long molecular-dynamics simulations of ∼1,000,000 atoms models.

Nonlinear Network Description for Many-Body Quantum Systems in Continuous Space.

We show that the recently introduced iterative backflow wave function can be interpreted as a general neural network in continuum space with nonlinear functions in the hidden units. Using this wave function in variational Monte Carlo simulations of liquid ^{4}He in two and three dimensions, we typically find a tenfold increase in accuracy over currently used wave functions. Furthermore, subsequent stages of the iteration procedure define a set of increasingly good wave functions, each with its own variational energy and variance of the local energy: extrapolation to zero variance gives energies in close agreement with the exact values.

Real-time imaging of adatom-promoted graphene growth on nickel.

Single adatoms are expected to participate in many processes occurring at solid surfaces, such as the growth of graphene on metals. We demonstrate, both experimentally and theoretically, the catalytic role played by single metal adatoms during the technologically relevant process of graphene growth on nickel (Ni). The catalytic action of individual Ni atoms at the edges of a growing graphene flake was directly captured by scanning tunneling microscopy imaging at the millisecond time scale, while force field molecular dynamics and density functional theory calculations rationalize the experimental observations.

Nonadiabatic Breaking of Topological Pumping.

We study Thouless pumping out of the adiabatic limit. Our findings show that despite its topological nature, this phenomenon is not generically robust to nonadiabatic effects. Indeed, we find that the Floquet diagonal ensemble value of the pumped charge shows a deviation from the topologically quantized limit which is quadratic in the driving frequency for a sudden switch on of the driving.

Frictional lubricity enhanced by quantum mechanics.

The quantum motion of nuclei, generally ignored in the physics of sliding friction, can affect in an important manner the frictional dissipation of a light particle forced to slide in an optical lattice. The density matrix-calculated evolution of the quantum version of the basic Prandtl-Tomlinson model, describing the dragging by an external force of a point particle in a periodic potential, shows that purely classical friction predictions can be very wrong. The strongest quantum effect occurs not for weak but for strong periodic potentials, where barriers are high but energy levels in each well are discrete, and resonant Rabi or Landau-Zener tunneling to states in the nearest well can preempt classical stick-slip with nonnegligible efficiency, depending on the forcing speed.

Dynamics of correlation-frozen antinodal quasiparticles in superconducting cuprates.

Many puzzling properties of high-critical temperature () superconducting (HTSC) copper oxides have deep roots in the nature of the antinodal quasiparticles, the elementary excitations with wave vector parallel to the Cu-O bonds. These electronic states are most affected by the onset of antiferromagnetic correlations and charge instabilities, and they host the maximum of the anisotropic superconducting gap and pseudogap. We use time-resolved extreme-ultraviolet photoemission with proper photon energy (18 eV) and time resolution (50 fs) to disclose the ultrafast dynamics of the antinodal states in a prototypical HTSC cuprate.

Phase Diagram of Hydrogen and a Hydrogen-Helium Mixture at Planetary Conditions by Quantum Monte Carlo Simulations.

Understanding planetary interiors is directly linked to our ability of simulating exotic quantum mechanical systems such as hydrogen (H) and hydrogen-helium (H-He) mixtures at high pressures and temperatures. Equation of state (EOS) tables based on density functional theory are commonly used by planetary scientists, although this method allows only for a qualitative description of the phase diagram. Here we report quantum Monte Carlo (QMC) molecular dynamics simulations of pure H and H-He mixture.

Velocity dependence of sliding friction on a crystalline surface.

We introduce and study a minimal 1D model for the simulation of dynamic friction and dissipation at the atomic scale. This model consists of a point mass (slider) that moves over and interacts weakly with a linear chain of particles interconnected by springs, representing a crystalline substrate. This interaction converts a part of the kinetic energy of the slider into phonon waves in the substrate.

Smallest Archimedean Screw: Facet Dynamics and Friction in Multiwalled Nanotubes.

We identify a new material phenomenon, where minute mechanical manipulations induce pronounced global structural reconfigurations in faceted multiwalled nanotubes. This behavior has strong implications on the tribological properties of these systems and may be the key to understand the enhanced interwall friction recently measured for boron-nitride nanotubes with respect to their carbon counterparts. Notably, the fast rotation of helical facets in these systems upon coaxial sliding may serve as a nanoscale Archimedean screw for directional transport of physisorbed molecules.

Mottness at finite doping and charge-instabilities in cuprates.

The influence of the Mott physics on the doping-temperature phase diagram of copper oxides represents a major issue that is subject of intense theoretical and experimental effort. Here, we investigate the ultrafast electron dynamics in prototypical single-layer Bi-based cuprates at the energy scale of the O-2→Cu-3 charge-transfer (CT) process. We demonstrate a clear evolution of the CT excitations from incoherent and localized, as in a Mott insulator, to coherent and delocalized, as in a conventional metal.

Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics.

We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term.

Photoactivated processes in optical fibers: generation and conversion mechanisms of twofold coordinated Si and Ge atoms.

In this work we present an extensive investigation of nanoscale physical phenomena related to oxygen-deficient centers (ODCs) in silica and Ge-doped silica by means of first-principles calculations, including nudged-elastic band, electron paramagnetic resonance parameters calculations, and many-body perturbation theory (GW and Bethe-Salpeter equation) techniques. We show that by neutralizing positively charged oxygen monovacancies we can obtain model structures of twofold Si and Ge defects of which the calculated absorption spectra and singlet-to-triplet transitions are in excellent agreement with the experimental optical absorption and photo-luminescence data. In particular we provide an exhaustive analysis of the main exciton peaks related to the presence of twofold defects including long-range correlation effects.

Accelerating ab initio Molecular Dynamics and Probing the Weak Dispersive Forces in Dense Liquid Hydrogen.

We propose an ab initio molecular dynamics method, capable of dramatically reducing the autocorrelation time required for the simulation of classical and quantum particles at finite temperatures. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix S. Here, we apply this technique to both Lennard-Jones models, to demonstrate the accuracy and speeding-up of the sampling, and within a quantum Monte Carlo based wave function approach, for determining the phase diagram of high-pressure hydrogen with simulations much longer than the autocorrelation time.

Development of Site-Specific Mg(2+)-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations.

The vital contribution of Mg ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg exerts on its surrounding ligands in varying RNA coordination environments.

Markov state modeling of sliding friction.

Markov state modeling (MSM) has recently emerged as one of the key techniques for the discovery of collective variables and the analysis of rare events in molecular simulations. In particular in biochemistry this approach is successfully exploited to find the metastable states of complex systems and their evolution in thermal equilibrium, including rare events, such as a protein undergoing folding. The physics of sliding friction and its atomistic simulations under external forces constitute a nonequilibrium field where relevant variables are in principle unknown and where a proper theory describing violent and rare events such as stick slip is still lacking.

Toward Accurate Adsorption Energetics on Clay Surfaces.

Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions.

Field-Driven Mott Gap Collapse and Resistive Switch in Correlated Insulators.

Mott insulators are "unsuccessful metals" in which Coulomb repulsion prevents charge conduction despite a metal-like concentration of conduction electrons. The possibility to unlock the frozen carriers with an electric field offers tantalizing prospects of realizing new Mott-based microelectronic devices. Here we unveil how such unlocking happens in a simple model that shows the coexistence of a stable Mott insulator and a metastable metal.

Multiwalled nanotube faceting unravelled.

Nanotubes show great promise for miniaturizing advanced technologies. Their exceptional physical properties are intimately related to their morphological and crystal structure. Circumferential faceting of multiwalled nanotubes reinforces their mechanical strength and alters their tribological and electronic properties.

Nanoscale orbital excitations and the infrared spectrum of a molecular Mott insulator: A15-CsC.

The quantum physics of ions and electrons behind low-energy spectra of strongly correlated molecular conductors, superconductors and Mott insulators is poorly known, yet fascinating especially in orbitally degenerate cases. The fulleride insulator CsC (A15), one such system, exhibits infrared (IR) spectra with low temperature peak features and splittings suggestive of static Jahn-Teller distortions with a breakdown of orbital symmetry in the molecular site. That is puzzling, since there is no detectable static distortion, and because the features and splittings disappear upon modest heating, which they should not.

Correlation Effects in Scanning Tunneling Microscopy Images of Molecules Revealed by Quantum Monte Carlo.

Scanning tunneling microscopy (STM) and spectroscopy probe the local density of states of single molecules electrically insulated from the substrate. The experimental images, although usually interpreted in terms of single-particle molecular orbitals, are associated with quasiparticle wave functions dressed by the whole electron-electron interaction. Here we propose an ab initio approach based on quantum Monte Carlo to calculate the quasiparticle wave functions of molecules.

Enzymatic and Inhibition Mechanism of Human Aromatase (CYP19A1) Enzyme. A Computational Perspective from QM/MM and Classical Molecular Dynamics Simulations.

The enzyme human aromatase (HA), a member of the cytochrome P450 family, catalyses in a highly specific and peculiar manner the conversion of estrogens to androgens. Thus, this enzyme is a relevant target for inhibitor design for the treatment of breast cancer and currently there are several HA inhibitors employed in clinical practice. The HA crystal structure was solved only in 2009 and, since then, several studies have been done to characterize a variety of its structural, dynamical and mechanistic properties.

Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns.

Group II introns are Mg(2+)-dependent ribozymes that are considered to be the evolutionary ancestors of the eukaryotic spliceosome, thus representing an ideal model system to understand the mechanism of conversion of premature messenger RNA (mRNA) into mature mRNA. Neither in splicing nor for self-cleaving ribozymes has the role of the two Mg(2+) ions been established, and even the way the nucleophile is activated is still controversial. Here we employed hybrid quantum-classical QM(Car-Parrinello)/MM molecular dynamics simulations in combination with thermodynamic integration to characterize the molecular mechanism of the first and rate-determining step of the splicing process (i.

Communication: Enhanced chemical reactivity of graphene on a Ni(111) substrate.

Due to the unique combination of structural, mechanical, and transport properties, graphene has emerged as an exceptional candidate for catalysis applications. The low chemical reactivity caused by sp(2) hybridization and strongly delocalized π electrons, however, represents a main challenge for straightforward use of graphene in its pristine, free-standing form. Following recent experimental indications, we show that due to charge hybridization, a Ni(111) substrate can enhance the chemical reactivity of graphene, as exemplified by the interaction with the CO molecule.