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Nitrogenase is the only enzyme that can convert N2 into NH3. The reaction requires the addition of eight electrons and protons to the enzyme and the mechanism is normally described by nine states, E0–E8, differing in the number of added electrons. Experimentally, it is known that three or four electrons need to be added before the enzyme can bind N2. We have used combined quantum mechanical and mo
Exoplanets in the ultra-hot Jupiter regime provide an excellent laboratory for testing the impact of stellar irradiation on the dynamics and chemical composition of gas giant atmospheres. In this study, we observed two transits of the ultra-hot Jupiter WASP-189 b with MAROON-X/Gemini-North to probe its high-altitude atmospheric layers, using strong absorption lines. We derived posterior probabilit
During protoplanetary disk formation, dust grains located in the outer disk retain their pristine icy composition, while solids in the inner stellar-heated disk undergo volatile loss. This process may have left a fossil record in Solar System material, showing different nucleosynthetic imprints that have been attributed to different degrees of thermal processing. However, it remains unclear how a
Free energy calculations play a crucial role in simulating chemical processes, enzymatic reactions, and drug design. However, assessing the reliability and convergence of these calculations remains a challenge. This study focuses on single-step free-energy calculations using thermodynamic perturbation. It explores how the sample distributions influence the estimated results and evaluates the relia
We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E2–E4 states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We
Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological life. Despite extensive research, the mechanism of nitrogen fixation by nitrogenase is not fully understood, partly due to the enzyme’s complex structure, which includes the largest iron–sulfur cluster known in metalloenzymes, the FeMo cluster. Understanding this process requires t
This work presents large-scale elasto-plastic topology optimization for design of structures with maximized energy absorption and tailored mechanical response. The implementation uses parallel computations to address multi million element three-dimensional problems. Design updates are generated using the gradient-based method of moving asymptotes and the material is modeled using small strain, non
In this fourth paper from the AGORA Collaboration, we study the evolution down to redshift z = 2 and below of a set of cosmological zoom-in simulations of a Milky Way mass galaxy by eight of the leading hydrodynamic simulation codes. We also compare this CosmoRun suite of simulations with dark matter-only simulations by the same eight codes. We analyze general properties of the halo and galaxy at
We have studied the conversion of two molecules of carbon monoxide to ethylene catalyzed by nitrogenase. We start from a recent crystal structure showing the binding of two carbon monoxide molecules to nitrogenase and employ the combined quantum mechanics and molecular mechanics approach. Our results indicate that the reaction is possible only if S2B dissociates as H2S (i.e., the charge of the FeM
The stimulator of interferon genes (STING) plays a significant role in immune defense and protection against tumor proliferation. Many cyclic dinucleotide (CDN) analogues have been reported to regulate its activity, but the dynamic process involved when the ligands activate STING remains unclear. In this work, all-atom molecular dynamics simulations were performed to explore the binding mode betwe
Recent observations of high-redshift galaxies (z ≲ 7) reveal that a substantial fraction have turbulent, gas-rich disks with well-ordered rotation and elevated levels of star formation. In some instances, disks show evidence of spiral arms, with bar-like structures. These remarkable observations have encouraged us to explore a new class of dynamically self-consistent models using our agama/Ramses
During their formation, nascent planetary systems are subject to FU Orionis outbursts that heat a substantial part of the disc. This causes water ice in the affected part of the disc to sublimate as the ice line moves outwards to several to tens of astronomical units. In this paper, we investigate how the subsequent cooling of the disc impacts the particle sizes. We calculate the resulting particl
The architecture and masses of planetary systems in the habitable zone could be strongly influenced by the presence of outer giant planets. Here, we investigate the impact of outer giants on terrestrial planet formation, under the assumption that the final assembly of the planetary system is set by a giant impact phase. Utilizing a state-of-the-art N-body simulation software, GENGA, we interpret h
The clumpy nature of gas-rich galaxies at cosmic noon raises the question of universality of the scaling relations and average properties of the star-forming structures. Using controlled simulations of disk galaxies and varying only the gas fraction, we show that the influence of the galactic environments (large-scale turbulence, tides, and shear) contributes, together with the different regime of
The aerobic oxidation of carbon monoxide to carbon dioxide is catalysed by the Mo/Cu-containing CO-dehydrogenase enzyme in the soil bacterium Oligotropha carboxidovorans, enabling the organism to grow on the small gas molecule as carbon and energy source. It was shown experimentally that silver can be substituted for copper in the active site of Mo/Cu CODH to yield a functional enzyme. In this stu
INTRODUCTION: The primary objective was to map the impact on confidence and performance on radiographic examinations among undergraduate radiography students utilizing virtual reality (VR). The secondary objective was to identify potential pitfalls to avoid in future VR implementation.METHODS: A systematic review was conducted, which included comprehensive search in nine databases. The software Co
An efficient extension of conventional rate-dependent crystal plasticity is formulated to include the influence of block boundaries in lath martensite. It is shown that this can be achieved by minor modifications to a conventional crystal plasticity model, providing an efficient modeling approach with a negligible additional computational cost. With this modification, the parameter related to latt
Topology optimization is a mathematical tool for the computational design of structures,particularly valuable in the early stages of the design process. Gradient-basedoptimization methods, combined with finite element analysis, form the foundation ofan iterative procedure where the design is continuously updated and evaluated. To expandthe applicability of topology optimization, this thesis explor
A novel regularization method for shape optimization of contacting structures is proposed. The shape optimization avoids parameterizations via splines or the level set method by directly optimizing the nodes in the finite element mesh. In the past this approach was limited by numerical difficulties arising from mesh entanglement and serrated boundaries but recent advances in regularization techniq
Interpretation of data from faint dwarf galaxies is made challenging by observations limited to only the brightest stars. We present a major improvement to tackle this challenge by undertaking zoomed cosmological simulations that resolve the evolution of all individual stars more massive than 0.5 M⊙, thereby explicitly tracking all observable stars for the Hubble time. For the first time, we predi
