Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution.

Dissecting human neurobiology at high resolution and with mechanistic precision requires a major leap in scalability, given the need for experimental designs that include multiple individuals and, prospectively, population cohorts. To lay the foundation for this, we have developed and benchmarked complementary strategies to multiplex brain organoids by pooling cells from different pluripotent stem cell (PSC) lines either during organoid generation (mosaic models) or before single-cell RNA sequencing (scRNA-seq) library preparation (downstream multiplexing). We have also developed a new computational method, SCanSNP, and a consensus call to deconvolve cell identities, overcoming current criticalities in doublets and low-quality cell identification.

RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fueled the COVID-19 pandemic with its enduring medical and socioeconomic challenges because of subsequent waves and long-term consequences of great concern. Here, we chart the molecular basis of COVID-19 pathogenesis by analyzing patients' immune responses at single-cell resolution across disease course and severity. This approach confirms cell subpopulation-specific dysregulation in COVID-19 across disease course and severity and identifies a severity-associated activation of the receptor for advanced glycation endproducts (RAGE) pathway in monocytes.

Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM.

We present a series of new implementations that we recently introduced in COBRAMM, the open-source academic software developed in our group. The goal of these implementations is to offer an automatized workflow and interface to simulate time-resolved transient absorption (TA) spectra of medium-to-big chromophore embedded in a complex environment. Therefore, the excited states absorption and the stimulated emission are simulated along nonadiabatic dynamics performed with trajectory surface hopping.

QM/MM Nonadiabatic Dynamics: the SHARC/COBRAMM Approach.

We present the SHARC/COBRAMM approach to enable easy and efficient excited-state dynamics simulations at different levels of electronic structure theory in the presence of complex environments using a quantum mechanics/molecular mechanics (QM/MM) setup. SHARC is a trajectory surface-hoping method that can incorporate the simultaneous effects of nonadiabatic and spin-orbit couplings in the excited-state dynamics of molecular systems. COBRAMM allows ground- and excited-state QM/MM calculations using a subtractive scheme, with electrostatic embedding and a hydrogen link-atom approach.

Spectral Tuning and Photoisomerization Efficiency in Push-Pull Azobenzenes: Designing Principles.

This work demonstrates how - substitution can induce spectral tuning toward the visible range and improve the photoisomerization efficiency of azobenzene-based photoswitches, making them good candidates for technological and biological applications. The red-shifted bright ππ* state (S) behaves like the lower and more productive dark nπ* (S) state because less potential energy along the planar bending mode is available to reach higher energy unproductive nπ*/S crossing regions, which are responsible for the lower quantum yield of the parent compound. The stabilization of the bright ππ* state and the consequent increase in isomerization efficiency may be regulated the strength of - substituents.

Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering.

Controlling the spectral tunability and isomerization activity is currently one of the hot topics in the design of photoreversible molecular switches for application in optoelectronic devices. The present work demonstrates how to manipulate the absorption of the retinal protonated Schiff base (rPSB) chromophore over the entire visible range by targeted functionalization of the retinal backbone. Moreover, a correlation between the vertical excitation energy and the profile of the potential energy surface of the bright excited state responsible for the photoreactivity of rPSB is established.

First-principles description of intra-chain exciton migration in an oligo(para-phenylene vinylene) chain. I. Generalized Frenkel-Holstein Hamiltonian.

A generalized Frenkel-Holstein Hamiltonian is constructed to describe exciton migration in oligo(para-phenylene vinylene) chains, based on excited state electronic structure data for an oligomer comprising 20 monomer units (OPV-20). Time-dependent density functional theory calculations using the ωB97XD hybrid functional are employed in conjunction with a transition density analysis to study the low-lying singlet excitations and demonstrate that these can be characterized to a good approximation as a Frenkel exciton manifold. Based on these findings, we employ the analytic mapping procedure of Binder et al.

To bend or not to bend, the dilemma of multiple bonds.

Beyond the second row of the periodic table, the nature of the multiple bonds between the elements of the main groups remains yet elusive, and "non-classical" bonding schemes are often invoked for their description. Here, focusing on group 14, we have performed an accurate modeling of the Si-Si and C-C double bonds, including electron correlation effects. We have shown that Si[double bond, length as m-dash]Si bonds are "classical" and closely resemble C[double bond, length as m-dash]C ones, being similarly subjected to a sort of tug of war in which the σ bond favors distortion and the π bond opposes it.

Multi-configurational Ehrenfest simulations of ultrafast nonadiabatic dynamics in a charge-transfer complex.

Multi-configurational Ehrenfest (MCE) approaches, which are intended to remedy the lack of correlations in the standard mean-field Ehrenfest method, have been proposed as coherent-state based for quantum propagation [D. V. Shalashilin, J.

Computation of the S ← S Vibronic Absorption Spectrum of Formaldehyde by Variational Gaussian Wavepacket and Semiclassical IVR Methods.

The vibronic absorption spectrum of the electric dipole forbidden and vibronically allowed S( A) ← S( A) transition of formaldehyde is calculated by Gaussian wavepacket and semiclassical methods, along with numerically exact reference calculations, using the potential energy surface of Fu, Shepler, and Bowman ( J. Am. Chem.

Sticking of atomic hydrogen on graphene.

Recent years have witnessed an ever growing interest in the interactions between hydrogen atoms and a graphene sheet. Largely motivated by the possibility of modulating the electric, optical and magnetic properties of graphene, a huge number of studies have appeared recently that added to and enlarged earlier investigations on graphite and other carbon materials. In this review we give a glimpse of the many facets of this adsorption process, as they emerged from these studies.

Full quantum dynamical investigation of the Eley-Rideal reaction forming H on a movable graphitic substrate at T = 0 K.

The dynamics of the Eley-Rideal abstraction reaction of hydrogen atoms on a movable graphitic surface is investigated for the first time in a numerically exact fully quantum setting. A system-bath strategy was applied where the two recombining H atoms and a substrate C atom form a relevant subsystem, while the rest of the lattice takes the form of an independent oscillator bath. High-dimensional wavepacket simulations were performed in the collision energy range 0.

Hydrogen on silicene: like or unlike graphene?

Hydrogenation of free-standing silicene, the two-dimensional allotrope of silicon, is investigated in detail using first-principles methods and compared with the adsorption of H atoms on graphene. Similarly to graphene, chemisorption of a single H atom on silicene induces the formation of a semilocalized state around the adatom, a sharp peak in the density of states at the Fermi level which acts as a strong resonant scatterer for charge carriers. This state hosts an unpaired electron, the itinerant electron of the resonating valence bond picture which primarily resides on the "majority" sublattice and biases the reactivity towards specific lattice positions.

Quantum dynamical investigation of the isotope effect in H2 formation on graphite at cold collision energies.

The Eley-Rideal abstraction of hydrogen atoms on graphitic surfaces at cold collision energies was investigated using a time-dependent wave packet method within the rigid-flat surface approximation, with a focus on hydrogen-deuterium isotopic substitutions. It is found that the marked isotope effect of collinear collisions disappears when the full dimensionality of the problem is taken into account, thereby suggesting that abstraction is less direct than commonly believed and proceeds through glancing rather than head-on collisions. In contrast, a clear isotope effect is observed for "hot-atom" formation, which appears to be strongly favored for heavy projectiles because of their higher density of physisorbed states.

Methane dissociation on Pt(111): Searching for a specific reaction parameter density functional.

The theoretical description of methane dissociating on metal surfaces is a current frontier in the field of gas-surface dynamics. Dynamical models that aim at achieving a highly accurate description of this reaction rely on potential energy surfaces based on density functional theory calculations at the generalized gradient approximation. We focus here on the effect that the exchange-correlation functional has on the reactivity of methane on a metal surface, using CHD3 + Pt(111) as a test case.

Quantum dynamics of hydrogen atoms on graphene. II. Sticking.

Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion.

Adiabatic potential energy surfaces for the low-energy collisional dynamics of C(+)((2)P) ions with H2 molecules.

The low-energy electronic states of the CH2(+) molecular ion are investigated with multireference configuration interaction calculations based on complete active space self-consistent field reference wave functions using a large C(6s5p4d3f)/H(8s6p3d1f) basis set. The focus is on the three lowest-lying states describing formation and destruction of the astrophysically relevant methylidine cation CH(+). Both processes are discussed in light of the topology of the relevant potential energy surfaces and their intersections.

From sniffer dogs to emerging sniffer devices for airport security: an opportunity to rethink privacy implications?

Dogs are known for their incredible ability to detect odours, extracting them from a "complex" environment and recognising them. This makes sniffer dogs precious assets in a broad variety of security applications. However, their use is subject to some intrinsic restrictions.

Thermal lattice expansion effect on reactive scattering of H2 from Cu(111) at T(s) = 925 K.

Surface phonons and surface temperature may have important effects on reactions of molecules at surfaces, and at present much remains unknown about these effects. A question addressed here, which has received little attention so far, is how reaction at elevated temperature is affected by thermal lattice expansion. To answer this question for the benchmark reaction of H2 and D2 with Cu(111), we have performed quantum and quasi-classical dynamics calculations.

Societal and ethical implications of anti-spoofing technologies in biometrics.

Biometric identification is thought to be less vulnerable to fraud and forgery than are traditional forms of identification. However biometric identification is not without vulnerabilities. In a 'spoofing attack' an artificial replica of an individual's biometric trait is used to induce a system to falsely infer that individual's presence.

Surface models and reaction barrier in Eley-Rideal formation of H2 on graphitic surfaces.

The exothermic, collinearly-dominated Eley-Rideal hydrogen formation on graphite is studied with electronic structure and quantum dynamical means. In particular, the focus is on the importance of the model used to describe the graphitic substrate, in light of the marked discrepancies present in available literature results. To this end, the collinear reaction is considered and the potential energy surface is computed for a number of different graphitic surface models using Density Functional Theory (DFT) for different dynamical regimes.

Hydrogen dissociation on Cu(111): the influence of lattice motion. Part I.

We have studied the effect of lattice displacement on the interaction of H(2) with the Cu(111) surface using the Specific Reaction Parameter (SRP) approach to Density Functional Theory (DFT). We have systematically investigated how the motion of the surface atoms affects some features of the Potential Energy Surface (PES), such as the dissociation barrier height and the barrier geometry corresponding to some representative reaction pathways, and the anisotropy of the potential at these geometries. This analysis has allowed us to identify the surface degrees of freedom that are likely to be most relevant for H(2) dissociation.