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Context. Several works have found an increase of the abundances of the s-process neutron-capture elements in the youngest Galactic stellar populations. These trends provide important constraints on stellar and Galactic evolution and they need to be confirmed with large and statistically significant samples of stars spanning wide age and distance intervals. Aims. We aim to trace the abundance patte
We have estimated free energies for the binding of eight carboxylate ligands to two variants of the octa-acid deep-cavity host in the SAMPL6 blind-test challenge (with or without endo methyl groups on the four upper-rim benzoate groups, OAM and OAH, respectively). We employed free-energy perturbation (FEP) for relative binding energies at the molecular mechanics (MM) and the combined quantum mecha
Formate dehydrogenases (FDHs) are metalloenzymes that catalyse the reversible conversion of formate to carbon dioxide. Since such a process may be used to combat the greenhouse effect, FDHs have been extensively studied by experimental and theoretical methods. However, the reaction mechanism is still not clear; instead five putative mechanisms have been suggested. In this work, the reaction mechan
Conceptual design is the first phase in the design process in which all the requirements and design objectives are synthesized into conceptual alternatives. In practice today, major decisions regarding the buildings function, massing, and overall form are usually made during the first phase. Considering structural performance requirements during conceptual design enhances interdisciplinary interac
A key step to the strut-and-tie method is the selection of an appropriate truss model, due to the static indeterminacy of reinforced concrete there are often several suitable models possible. A method for automatically generating a suitable truss model by using graphic statics is presented. Optimal layouts are found by minimizing the total load path. A formulation of constraints suitable for gener
We show how a multi-resolution network can model the development of acuity and coarse-to-fine processing in the mammalian visual cortex. The network adapts to input statistics in an unsupervised manner, and learns a coarse-to-fine representation by using cumulative inhibition of nodes within a network layer. We show that a system of such layers can represent input by hierarchically composing large
The radial drift and diffusion of dust particles in protoplanetary disks affect both the opacity and temperature of such disks, as well as the location and timing of planetesimal formation. In this paper, we present results of numerical simulations of particle-gas dynamics in protoplanetary disks that include dust grains with various size distributions. We have considered three scenarios in terms
Isothermal titration calorimetry (ITC) is an apt tool for a total thermodynamic description of self-assembly of atypical amphiphiles such as anionic boron cluster compounds (COSAN) in water. Global fitting of ITC enthalpograms reveals remarkable features that differentiate COSAN from classical amphiphiles: (i) strong enthalpy and weak entropy contribution to the free energy of aggregation, (ii) lo
In the era of large-scale surveys of stars in the MilkyWay, stellar ages are crucial for studying the evolution of the Galaxy.But determining ages of field stars is notoriously difficult; therefore, we attempt to determine benchmark ages for the extensively studied Gaia benchmark stars which can be used for validation purposes. By searching the literature for age estimates from different methods a
The streaming instability is a promising mechanism to drive the formation of planetesimals in protoplanetary disks. To trigger this process, it has been argued that sedimentation of solids onto the mid-plane needs to be efficient, and therefore that a quiescent gaseous environment is required. It is often suggested that dead-zone or disk-wind structure created by non-ideal magnetohydrodynamical (M
Donor-acceptor (D-A) copolymers typically show two absorption peaks in the visible region, flanking a valley region of limited absorptivity. One strategy for more panchromatic light harvesting is to incorporate side-groups orthogonal to the polymer backbone, which enable 2D π conjugation and can give rise to additional absorption peaks. Here we design and synthesize two D-A polymers which both car
[NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular m
We have performed a systematic computational study of the relative energies of possible protonation states of the FeMo cluster in nitrogenase in the E0-E4 states, i.e., the resting state and states with 1-4 electrons and protons added but before N2 binds. We use the combined quantum mechanics and molecular mechanics (QM/MM) approach, including the complete solvated heterotetrameric enzyme in the c
Attractive interactions between intrinsically disordered proteins can be crucial for the functionality or, on the contrary, lead to the formation of harmful aggregates. For obtaining a molecular understanding of intrinsically disordered proteins and their interactions, computer simulations have proven to be a valuable complement to experiments. In this study, we present a coarse-grained model and
Objectives: To determine predictors of renal relapse and end-stage renal failure (ESRF) in patients with ANCA-associated vasculitis. Methods: Data from four European Vasculitis Society randomized controlled trials, conducted roughly simultaneously between 15 March 1995 and 30 September 2002, was pooled to determine predictors of long-term renal outcome. The respective trial inclusion criteria cove
Molecular-level computer simulations of peptide aggregation, translocation, and protonation at and in biomembranes are impeded by the large time and length scales involved. We present a computationally efficient, coarse-grained, and solvent-free model for the interaction between lipid bilayers and peptides. The model combines an accurate description of mechanical membrane properties with a new gra
We describe how an arousal system that controls the levels of awareness can be implemented in a robot. The different levels of awareness correspond to different states of consciousness and we argue that an artificial arousal system modeled after its biological counterpart has a useful function in controlling the cognitive processing of a brain-like cognitive architecture. The level of awareness de
Calculating binding free energies with quan-tum-mechanical (QM) methods is notoriously time-consum-ing. In this work, we studied whether such calculations can beaccelerated by using nonequilibrium (NE) moleculardynamics simulations employing Jarzynski’s equality. Westudied the binding of nine cyclic carboxylate ligands to theocta-acid deep-cavity host from the SAMPL4 challenge withthe reference po
The enzyme nitrogenase contains a complicated MoFe7CS9 cofactor with 35 possible broken- symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one- electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Lik
We have devised a new efficient approach tocompute combined quantum mechanical (QM) and molecularmechanical (MM, i.e. QM/MM) ligand-binding relative freeenergies. Our method employs the reference-potentialapproach with free-energy perturbation both at the MMlevel (between the two ligands) and from MM to QM/MM(for each ligand). To ensure that converged results areobtained for the MM → QM/MM perturb
