Multiscale Modeling of Electronic Spectra Including Nuclear Quantum Effects

<div>Theoretical prediction of electronic absorption spectra without input from experiment is no easy feat as it requires addressing all the factors that affect line shapes. In practice, however, the methodologies are limited to treat these ingredients only to a certain extent. Here we present a multiscale protocol that addresses the temperature, solvent and nuclear quantum effects, anharmonicity and reconstruction of the final spectra from the individual transitions. First, QM/MM molecular dynamics is conducted to obtain trajectories of solute-solvent configurations, from which the corresponding quantum corrected ensembles are generated through the Generalized Smoothed Trajectory Analysis (GSTA). The optical spectra of the ensembles are then produced by calculating vertical transitions using TDDFT with implicit solvation. To obtain the final spectral shapes, the stick spectra from TDDFT are convoluted with Gaussian kernels where the half-widths are determined by a statistically motivated strategy. We have tested our method by calculating the UV-vis spectra of a recently discovered acridine photocatalyst in two redox states and evaluated the impact of each step. Nuclear quantization affects the relative peak intensities and widths, which is necessary to reproduce the experimental spectrum. We have also found that using only the optimized geometry of each molecule works surprisingly well if a proper empirical broadening factor is applied. This is explained by the rigidity of the conjugated chromophore moieties of the selected molecules which are mainly responsible for the excitations in the spectra. In contrast, we have also shown that the molecules are flexible enough to feature anharmonicities that impair the Wigner sampling. </div>

Multiscale Modeling of Electronic Spectra Including Nuclear Quantum Effects

<div>Theoretical prediction of electronic absorption spectra without input from experiment is no easy feat as it requires addressing all the factors that affect line shapes. In practice, however, the methodologies are limited to treat these ingredients only to a certain extent. Here we present a multiscale protocol that addresses the temperature, solvent and nuclear quantum effects, anharmonicity and reconstruction of the final spectra from the individual transitions. First, QM/MM molecular dynamics is conducted to obtain trajectories of solute-solvent configurations, from which the corresponding quantum corrected ensembles are generated through the Generalized Smoothed Trajectory Analysis (GSTA). The optical spectra of the ensembles are then produced by calculating vertical transitions using TDDFT with implicit solvation. To obtain the final spectral shapes, the stick spectra from TDDFT are convoluted with Gaussian kernels where the half-widths are determined by a statistically motivated strategy. We have tested our method by calculating the UV-vis spectra of a recently discovered acridine photocatalyst in two redox states and evaluated the impact of each step. Nuclear quantization affects the relative peak intensities and widths, which is necessary to reproduce the experimental spectrum. We have also found that using only the optimized geometry of each molecule works surprisingly well if a proper empirical broadening factor is applied. This is explained by the rigidity of the conjugated chromophore moieties of the selected molecules which are mainly responsible for the excitations in the spectra. In contrast, we have also shown that the molecules are flexible enough to feature anharmonicities that impair the Wigner sampling. </div>

Effects of Rearing Aviary Style and Genetic Strain on the Locomotion and Musculoskeletal Characteristics of Layer Pullets

Previous research indicates that the musculoskeletal development of pullets is improved when pullets are reared in aviaries compared to conventional rearing cages. However, there are considerable differences in rearing aviary design. To measure locomotion and musculoskeletal development of brown (n = 7) and white-feathered (n = 8) strains of pullets, 15 commercial flocks in three styles of rearing aviaries differing in structural complexity (n = 5 per style) were visited three times: 25.9 ± 6.67, 68.0 ± 4.78, and 112.1 ± 3.34 days of age. Locomotion (duration of standing, sitting, walking, running, flying, and rates jumping, flying, group running and walking) was analysed from videos recorded three times per day: at the beginning, middle, and end of the light cycle. Pullets for dissection were taken on visits 2 and 3. Pullets in the most complex system (style 3; S3) spent the most time locomoting throughout rearing (p < 0.05). Pullets in S3, particularly white-feathered strains, performed the highest rate of vertical transitions (p < 0.05). There were no differences in any of the proportional muscle weights between aviaries styles (p > 0.05) despite the differences in locomotion. White-feathered strains, however, had proportionally heavier pectoralis major (p < 0.0001), pectoralis minor (p < 0.0001), and lighter leg muscles (p < 0.0001) than brown-feathered strains. White-feathered strains and pullets in S3 also had proportionally stronger tibiae and femurs than brown-feathered strains and pullets housed in the least structurally complex system (style 1; S1) (p < 0.05). However, there were no differences found in the breaking strength of the radius and humerus between strain colours or aviary styles (p < 0.05). Therefore, strain, as well as differences in rearing aviary design, can affect the types of locomotion that growing pullets perform, which may, in turn, impact their skeletal development.

Deep impact of superficial skin inking: acoustic analysis of underlying tissue

Background: Skin tattoos are a common decoration, but profound scientific study whether the presence of a skin tattoo alters the acoustic response from superficial tissue, and therefore from underlying tissue, was previously lacking. Any image aberrations caused by tattoo presence may have been thought negligible, yet empirically found artifacts in brightness-mode images of tattooed skin suggest otherwise. This study investigated the nature of these artifacts theoretically and experimentally in extremely simplified cases of perfectly flat and homogenous layered media and in tattooed pork.Methods: Theory was derived for computing the acoustic response from horizontally and vertically layered media containing a thin inked layer. Experiments were performed in vitro. Artificial and pork skin were tattooed, attached to phantom material, and sonicated with a 13–6-MHz probe. The speed of sound of these materials was determined, and the perceived refraction angles was measured.Results: The measured speeds of sound of tattooed materials were higher than those of their uninked counterparts. The presence of tattoo ink was found to have increased the linear acoustic attenuation by 1 dB/cm. This value is negligible for typical tattoos of only few millimeters. The perceived critical refraction angles of adjacent materials could be detected, and their corresponding speeds of sound were quantified. These coincided with values derived from theory.Conclusion: The ratio of speeds of sound of adjacent materials was shown to create distinct highlights in brightness-mode images. The artifacts observed in in vitro and in vivo brightness-mode scans were explained from near-vertical transitions between areas of different sound speed. This is the first study correlating so-called critical refraction highlighting with speed-of-sound information. In addition, it was found that phantom material is a room-temperature acoustic alternative for experiments on live human skin. In summary, the presence of superficial tattoos has a small but quantifiable effect on the acoustic response from deeper tissues.

Transition by head-on collision: mechanically mediated manoeuvres in cockroaches and small robots

Exceptional performance is often considered to be elegant and free of ‘errors’ or missteps. During the most extreme escape behaviours, neural control can approach or exceed its operating limits in response time and bandwidth. Here we show that small, rapid running cockroaches with robust exoskeletons select head-on collisions with obstacles to maintain the fastest escape speeds possible to transition up a vertical wall. Instead of avoidance, animals use their passive body shape and compliance to negotiate challenging environments. Cockroaches running at over 1 m or 50 body lengths per second transition from the floor to a vertical wall within 75 ms by using their head like an automobile bumper, mechanically mediating the manoeuvre. Inspired by the animal's behaviour, we demonstrate a passive, high-speed, mechanically mediated vertical transitions with a small, palm-sized legged robot. By creating a collision model for animal and human materials, we suggest a size dependence favouring mechanical mediation below 1 kg that we term the ‘Haldane limit’. Relying on the mechanical control offered by soft exoskeletons represents a paradigm shift for understanding the control of small animals and the next generation of running, climbing and flying robots where the use of the body can off-load the demand for rapid sensing and actuation.