SOFI: Finding point group symmetries in atomic clusters as finding the set of degenerate solutions in a shape-matching problem.

Point Group (PG) symmetries play a fundamental role in many aspects of theoretical chemistry and computational materials science. With the objective to automatize the search of PG symmetry operations of generic atomic clusters, we present a new algorithm called Symmetry Operation FInder (SOFI). SOFI addresses the problem of identifying PG symmetry by framing it as a degenerate shape-matching problem, where the multiple solutions correspond to distinct symmetry operations.

Exploring potential energy surfaces to reach saddle points above convex regions.

Saddle points on high-dimensional potential energy surfaces (PES) play a determining role in the activated dynamics of molecules and materials. Building on approaches dating back more than 50 years, many open-ended transition-state search methods have been developed to follow the direction of negative curvature from a local minimum to an adjacent first-order saddle point. Despite the mathematical justification, these methods can display a high failure rate: using small deformation steps, up to 80% of the explorations can end up in a convex region of the PES, where all directions of negative curvature vanish, while if the deformation is aggressive, a similar fraction of attempts lead to saddle points that are not directly connected to the initial minimum.

Parent Hamiltonian Reconstruction via Inverse Quantum Annealing.

Finding a local Hamiltonian H[over ^] that has a given many-body wave function |ψ⟩ as its ground state, i.e., a parent Hamiltonian, is a challenge of fundamental importance in quantum technologies.

The Influence of Catechols on the Magnetization of Iron Oxide Nanoparticles.

In this study, MNPs were functionalized with pyrocatechol (CAT), pyrogallol (GAL), caffeic acid (CAF), and nitrodopamine (NDA) at pH 8 and pH 11. The functionalization of the MNPs was successful, except in the case of NDA at pH 11. The thermogravimetric analyses indicated that the surface concentration of the catechols was between 1.

Saturation magnetisation as an indicator of the disintegration of barium hexaferrite nanoplatelets during the surface functionalisation.

Barium hexaferrite nanoplatelets (BHF NPLs) are permanent nanomagnets with the magnetic easy axis aligned perpendicular to their basal plane. By combining this specific property with optimised surface chemistry, novel functional materials were developed, e.g.

Molecular Basis of SARS-CoV-2 Nsp1-Induced Immune Translational Shutdown as Revealed by All-Atom Simulations.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic represents the most severe global health crisis in modern human history. One of the major SARS-CoV-2 virulence factors is nonstructural protein 1 (Nsp1), which, outcompeting with the binding of host mRNA to the human ribosome, triggers a translation shutdown of the host immune system. Here, microsecond-long all-atom simulations of the C-terminal portion of the SARS-CoV-2/SARS-CoV Nsp1 in complex with the 40S ribosome disclose that SARS-CoV-2 Nsp1 has evolved from its SARS-CoV ortholog to more effectively hijack the ribosome by undergoing a critical switch of Q/E158 and E/Q159 residues that perfects Nsp1's interactions with the ribosome.

Thermal dynamics and electronic temperature waves in layered correlated materials.

Understanding the mechanism of heat transfer in nanoscale devices remains one of the greatest intellectual challenges in the field of thermal dynamics, by far the most relevant under an applicative standpoint. When thermal dynamics is confined to the nanoscale, the characteristic timescales become ultrafast, engendering the failure of the common description of energy propagation and paving the way to unconventional phenomena such as wave-like temperature propagation. Here, we explore layered strongly correlated materials as a platform to identify and control unconventional electronic heat transfer phenomena.

IRA: A Shape Matching Approach for Recognition and Comparison of Generic Atomic Patterns.

We propose a versatile, parameter-less approach for solving the shape matching problem, specifically in the context of atomic structures when atomic assignments are not known a priori. The algorithm Iteratively suggests Rotated atom-centered reference frames and Assignments (iterative rotations and assignments (IRA)). The frame for which a permutationally invariant set-set distance, namely, the Hausdorff distance, returns a minimal value is chosen as the solution of the matching problem.

Peculiar Atomic Bond Nature in Platinum Monatomic Chains.

Metal atomic chains have been reported to change their electronic or magnetic properties by slight mechanical stimulus. However, the mechanical response has been veiled because of lack of information on the bond nature. Here, we clarify the bond nature in platinum (Pt) monatomic chains by our transmission electron microscope method.

Pervasive orientational and directional locking at geometrically heterogeneous sliding interfaces.

Understanding the drift motion and dynamical locking of crystalline clusters on patterned substrates is important for the diffusion and manipulation of nano- and microscale objects on surfaces. In a previous work, we studied the orientational and directional locking of colloidal two-dimensional clusters with triangular structure driven across a triangular substrate lattice. Here we show with experiments and simulations that such locking features arise for clusters with arbitrary lattice structure sliding across arbitrary regular substrates.

Atomic-Level Mechanism of Pre-mRNA Splicing in Health and Disease.

Intron removal from premature-mRNA (pre-mRNA splicing) is an essential part of gene expression and regulation that is required for the production of mature, protein-coding mRNA. The spliceosome (SPL), a majestic machine composed of five small nuclear RNAs and hundreds of proteins, behaves as an eminent transcriptome tailor, efficiently performing splicing as a protein-directed metallo-ribozyme. To select and excise long and diverse intronic sequences with single-nucleotide precision, the SPL undergoes a continuous compositional and conformational remodeling, forming eight distinct complexes throughout each splicing cycle.

Structural lubricity in soft and hard matter systems.

Over the recent decades there has been tremendous progress in understanding and controlling friction between surfaces in relative motion. However the complex nature of the involved processes has forced most of this work to be of rather empirical nature. Two very distinctive physical systems, hard two-dimensional layered materials and soft microscopic systems, such as optically or topographically trapped colloids, have recently opened novel rationally designed lines of research in the field of tribology, leading to a number of new discoveries.

Finding Reaction Pathways and Transition States: r-ARTn and d-ARTn as an Efficient and Versatile Alternative to String Approaches.

Finding transition states and diffusion pathways is essential to understand the evolution of materials and chemical reactions. Such characterization is hampered by the heavy computation costs associated with exploring energy landscapes at accuracy. Here, we revisit the activation-relaxation technique (ARTn) to considerably reduce its costs when used with the density functional theory and propose three adapted versions of the algorithm to efficiently (i) explore the energy landscape of complex materials with the knowledge of a single minimum (ARTn); (ii) identify a transition state when two minima or a guess transition state is given (refining ART or r-ART); and (iii) reconstruct complex pathways between two given states (directed ART or d-ART).

Collective dipole effects in ionic transport under electric fields.

In the context of ionic transport in solids, the variation of a migration barrier height under electric fields is traditionally assumed to be equal to the classical electric work of a point charge that carries the transport charge. However, how reliable is this phenomenological model and how does it fare with respect to Modern Theory of Polarization? In this work, we show that such a classical picture does not hold in general as collective dipole effects may be critical. Such effects are unraveled by an appropriate polarization decomposition and by an expression that we derive, which defines the equivalent polarization-work charge.

Pile-up transmission and reflection of topological defects at grain boundaries in colloidal crystals.

Crystalline solids typically contain large amounts of defects such as dislocations and interstitials. How they travel across grain boundaries (GBs) under external stress is crucial to understand the mechanical properties of polycrystalline materials. Here, we experimentally and theoretically investigate with single-particle resolution how the atomic structure of GBs affects the dynamics of interstitial defects driven across monolayer colloidal polycrystals.

Localization, Topology, and Quantized Transport in Disordered Floquet Systems.

We investigate the effects of disorder on a periodically driven one-dimensional model displaying quantized topological transport. We show that, while instantaneous eigenstates are necessarily Anderson localized, the periodic driving plays a fundamental role in delocalizing Floquet states over the whole system, henceforth allowing for a steady-state nearly quantized current. Remarkably, this is linked to a localization-delocalization transition in the Floquet states at strong disorder, which occurs for periodic driving corresponding to a nontrivial loop in the parameter space.

Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations.

The spliceosome accurately promotes precursor messenger-RNA splicing by recognizing specific noncoding intronic tracts including the branch point sequence (BPS) and the 3'-splice-site (3'SS). Mutations of Hsh155 (yeast)/SF3B1 (human), which is a protein of the SF3b factor involved in BPS recognition and induces altered BPS binding and 3'SS selection, lead to mis-spliced mRNA transcripts. Although these mutations recur in hematologic malignancies, the mechanism by which they change gene expression remains unclear.

Modeling nanoribbon peeling.

The lifting, peeling and exfoliation of physisorbed ribbons (or flakes) of 2D material such as graphene off a solid surface are common and important manoeuvres in nanoscience. The feature that makes this case peculiar is the structural lubricity generally realized by stiff 2D material contacts. We model theoretically the mechanical peeling of a nanoribbon of graphene as realized by the tip-forced lifting of one of its extremes off a flat crystal surface.

v-PO micro-clustering in P-doped silica studied by a first-principles Raman investigation.

Synthetic vitreous silica is currently the preferred material for the production of optical fibres because of the several excellent properties of this glass, e.g. high transmission in the visible and IR domains, high mechanical strength, chemical durability, and ease of doping with various materials.

Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.

Noncoding RNA (ncRNA) has a key role in regulating gene expression, mediating fundamental processes and diseases via a variety of yet unknown mechanisms. Here, we review recent applications of conventional and enhanced Molecular Dynamics (MD) simulations methods to address the mechanistic function of large biomolecular systems that are tightly involved in the ncRNA function and that are of key importance in life sciences. This compendium focuses of three biomolecular systems, namely the CRISPR-Cas9 genome editing machinery, group II intron ribozyme and the ribonucleoprotein complex of the spliceosome, which edit and process ncRNA.

Detachment Dynamics of Graphene Nanoribbons on Gold.

Metal-surface physisorbed graphene nanoribbons (GNRs) constitute mobile nanocontacts whose interest is simultaneously mechanical, electronic, and tribological. Previous work showed that GNRs adsorbed on Au(111) generally slide smoothly and superlubrically owing to the incommensurability of their structures. We address here the nanomechanics of detachment, as realized when one end is picked up and lifted by an AFM cantilever.

Angle-resolved photoemission spectroscopy from first-principles quantum Monte Carlo.

Angle-resolved photoemission spectroscopy allows one to visualize in momentum space the probability weight maps of electrons subtracted from molecules deposited on a substrate. The interpretation of these maps usually relies on the plane wave approximation through the Fourier transform of single particle orbitals obtained from density functional theory. Here we propose a first-principle many-body approach based on quantum Monte Carlo (QMC) to directly calculate the quasi-particle wave functions (also known as Dyson orbitals) of molecules in momentum space.

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.