MiMiC: A high-performance framework for multiscale molecular dynamics simulations.

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data (MPMD) paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.

From Chalcogen Bonding to S-π Interactions in Hybrid Perovskite Photovoltaics.

The stability of hybrid organic-inorganic halide perovskite semiconductors remains a significant obstacle to their application in photovoltaics. To this end, the use of low-dimensional (LD) perovskites, which incorporate hydrophobic organic moieties, provides an effective strategy to improve their stability, yet often at the expense of their performance. To address this limitation, supramolecular engineering of noncovalent interactions between organic and inorganic components has shown potential by relying on hydrogen bonding and conventional van der Waals interactions.

Multiscale biomolecular simulations in the exascale era.

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are crucial for capturing processes beyond the reach of classical MD simulations. The advent of exascale computing offers unprecedented opportunities for scientific exploration, not least within life sciences, where simulations are essential to unravel intricate molecular mechanisms underlying biological processes.

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach.

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to explain the high detection rate in the face of numerous, small lesions. The viability of CT DNA defect detection is explored via hybrid QM/MM computational studies that leverage the accuracy of quantum mechanics (QM) for a region of interest and the descriptive power of molecularmechanics (MM) for the remainder of the system.

Structure and dynamics of liquid water from simulations: adding Minnesota density functionals to Jacob's ladder.

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data.

Plane Waves Versus Correlation-Consistent Basis Sets: A Comparison of MP2 Non-Covalent Interaction Energies in the Complete Basis Set Limit.

Second-order Møller-Plesset perturbation theory (MP2) is the most expedient wave function-based method for considering electron correlation in quantum chemical calculations and, as such, provides a cost-effective framework to assess the effects of basis sets on correlation energies, for which the complete basis set (CBS) limit can commonly only be obtained via extrapolation techniques. Software packages providing MP2 energies are commonly based on atom-centered bases with innate issues related to possible basis set superposition errors (BSSE), especially in the case of weakly bonded systems. Here, we present noncovalent interaction energies in the CBS limit, free of BSSE, for 20 dimer systems of the S22 data set obtained via a highly parallelized MP2 implementation in the plane-wave pseudopotential molecular dynamics package CPMD.

Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations.

The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-containing NCP systems with an explicit representation of a biologically relevant environment. Two distinct NCP positions with varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that the presence of 8oxoG drastically decreases the redox free energy of oxidation by roughly 1 eV, which is very similar to what was recently reported for free native and 8oxoG-containing DNA.

Low-loss contacts on textured substrates for inverted perovskite solar cells.

Inverted perovskite solar cells (PSCs) promise enhanced operating stability compared to their normal-structure counterparts. To improve efficiency further, it is crucial to combine effective light management with low interfacial losses. Here we develop a conformal self-assembled monolayer (SAM) as the hole-selective contact on light-managing textured substrates.

Tautomeric mixture coordination enables efficient lead-free perovskite LEDs.

Lead halide perovskite light-emitting diodes (PeLEDs) have demonstrated remarkable optoelectronic performance. However, there are potential toxicity issues with lead and removing lead from the best-performing PeLEDs-without compromising their high external quantum efficiencies-remains a challenge. Here we report a tautomeric-mixture-coordination-induced electron localization strategy to stabilize the lead-free tin perovskite TEASnI (TEAI is 2-thiopheneethylammonium iodide) by incorporating cyanuric acid.

Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins.

Metal ions are essential cofactors for many proteins and play a crucial role in many applications such as enzyme design or design of protein-protein interactions because they are biologically abundant, tether to the protein using strong interactions, and have favorable catalytic properties. Computational design of metalloproteins is however hampered by the complex electronic structure of many biologically relevant metals such as zinc . In this work, we develop two tools - Metal3D (based on 3D convolutional neural networks) and Metal1D (solely based on geometric criteria) to improve the location prediction of zinc ions in protein structures.

MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations.

MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular mechanics, MM) codes. The code requires preparing separate input files for the two programs with a selection of the QM region.

Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures.

Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this work, we address the challenging task of efficiently sampling realistic low-lying peptide coordinates by resorting to a surrogate based genetic algorithm (GA)/density functional theory (DFT) approach (sGADFT) in which promising candidates provided by the GA are ultimately optimized with DFT.

Hydration dynamics and IR spectroscopy of 4-fluorophenol.

Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of -fluorophenol (F-PhOH) and phenol (PhOH) is investigated in the gas phase and in water using a combination of experiment and molecular dynamics (MD) simulations. The gas phase and solvent dynamics around F-PhOH and PhOH is characterized from atomistic simulations using empirical energy functions with point charges or multipoles for the electrostatics, Machine Learning (ML) based parametrizations and with full (QM) and mixed Quantum Mechanical/Molecular Mechanics (QM/MM) simulations with a particular focus on the CF- and OH-stretch region.

Interplay of Kinetic and Thermodynamic Reaction Control Explains Incorporation of Dimethylammonium Iodide into CsPbI.

CsPbI is a promising material for optoelectronics owing to its thermal robustness and favorable bandgap. However, its fabrication is challenging because its photoactive phase is thermodynamically unstable at room temperature. Adding dimethylammonium (DMA) alleviates this instability and is currently understood to result in the formation of DMA Cs PbI perovskite solid solutions.

Reversible Pressure-Dependent Mechanochromism of Dion-Jacobson and Ruddlesden-Popper Layered Hybrid Perovskites.

Layered Dion-Jacobson (DJ) and Ruddlesden-Popper (RP) hybrid perovskites are promising materials for optoelectronic applications due to their modular structure. To fully exploit their functionality, mechanical stimuli can be used to control their properties without changing the composition. However, the responsiveness of these systems to pressure compatible with practical applications (<1 GPa) remains unexploited.

A theoretical perspective of the ultrafast transient absorption dynamics of CsPbBr.

Transient absorption spectra (TAS) of lead halide perovskites can provide important insights into the nature of the photoexcited state dynamics of this prototypical class of materials. Here, we perform ground and excited state molecular dynamics (MD) simulations within a restricted open shell Kohn-Sham (ROKS) approach in order to interpret the characteristic features of the TAS of CsPbBr . Our results reveal that properties such as the finite temperature band gap, the Stokes shift, and therefore, also the TAS are strongly size-dependent.

A multiple time step algorithm for trajectory surface hopping simulations.

A multiple time step (MTS) algorithm for trajectory surface hopping molecular dynamics has been developed, implemented, and tested. The MTS scheme is an extension of the ab initio implementation for Born-Oppenheimer molecular dynamics presented in the work of Liberatore et al. [J.

Recent Advances in First-Principles Based Molecular Dynamics.

First-principles molecular dynamics (FPMD) and its quantum mechanical-molecular mechanical (QM/MM) extensions are powerful tools to follow the real-time dynamics of a broad variety of systems in their ground as well as electronically excited states. The continued advances in computational power have enabled simulations of QM regions of larger sizes for more extended time scales. In addition, development of the parallel algorithms has boosted the performance of QM/MM methods even on existing computer architectures.

A universal co-solvent dilution strategy enables facile and cost-effective fabrication of perovskite photovoltaics.

Cost management and toxic waste generation are two key issues that must be addressed before the commercialization of perovskite optoelectronic devices. We report a groundbreaking strategy for eco-friendly and cost-effective fabrication of highly efficient perovskite solar cells. This strategy involves the usage of a high volatility co-solvent, which dilutes perovskite precursors to a lower concentration (<0.

Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC.

We present an interface of the wavefunction-based quantum chemical software CFOUR to the multiscale modeling framework MiMiC. Electrostatic embedding of the quantum mechanical (QM) part is achieved by analytic evaluation of one-electron integrals in CFOUR, while the rest of the QM/molecular mechanical (MM) operations are treated according to the previous MiMiC-based QM/MM implementation. Long-range electrostatic interactions are treated by a multipole expansion of the potential from the QM electron density to reduce the computational cost without loss of accuracy.

Nanoscale interfacial engineering enables highly stable and efficient perovskite photovoltaics.

We present a facile molecular-level interface engineering strategy to augment the long-term operational and thermal stability of perovskite solar cells (PSCs) by tailoring the interface between the perovskite and hole transporting layer (HTL) with a multifunctional ligand 2,5-thiophenedicarboxylic acid. The solar cells exhibited high operational stability (maximum powering point tracking at one sun illumination) with a stabilized (the time over which the device efficiency reduces to 80% after initial burn-in) of ≈5950 h at 40 °C and a stabilized power conversion efficiency (PCE) over 23%. The origin of high device stability and performance is correlated to the nano/sub-nanoscale molecular level interactions between ligand and perovskite layer, which is further corroborated by comprehensive multiscale characterization.

Multimodal host-guest complexation for efficient and stable perovskite photovoltaics.

Formamidinium lead iodide perovskites are promising light-harvesting materials, yet stabilizing them under operating conditions without compromising optimal optoelectronic properties remains challenging. We report a multimodal host-guest complexation strategy to overcome this challenge using a crown ether, dibenzo-21-crown-7, which acts as a vehicle that assembles at the interface and delivers Cs ions into the interior while modulating the material. This provides a local gradient of doping at the nanoscale that assists in photoinduced charge separation while passivating surface and bulk defects, stabilizing the perovskite phase through a synergistic effect of the host, guest, and host-guest complex.

Ultrafast pulse shaping modulates perceived visual brightness in living animals.

Vision is usually assumed to be sensitive to the light intensity and spectrum but not to its spectral phase. However, experiments performed on retinal proteins in solution showed that the first step of vision consists in an ultrafast photoisomerization that can be coherently controlled by shaping the phase of femtosecond laser pulses, especially in the multiphoton interaction regime. The link between these experiments in solution and the biological process allowing vision was not demonstrated.