Vibrational spectroscopy by means of first-principles molecular dynamics simulations

Vibrational spectroscopy is one of the most important experimental techniques for the characterization of molecules and materials. Spectroscopic signatures retrieved in experiments are not always easy to explain in terms of the structure and dynamics of the studied samples. Computational studies are a crucial tool for helping to understand and predict experimental results. Molecular dynamics simulations have emerged as an attractive method for the simulation of vibrational spectra because they explicitly treat the vibrational motion present in the compound under study, in particular in large and condensed systems, subject to complex intramolecular and intermolecular interactions. In this context, first-principles molecular dynamics (FPMD) has been proven to provide an accurate realistic description of many compounds. This review article summarizes the field of vibrational spectroscopy by means of FPDM and highlights recent advances made such as the simulation of Infrared, vibrational circular dichroism, Raman, Raman optical activity, sum frequency generation, and nonlinear spectroscopies

Antifreeze Proteins in the Primary Urine of Larvae of the Beetle \u3cem\u3eDendroides canadensis\u3c/em\u3e

To avoid freezing while overwintering beneath the bark of fallen trees, Dendroides canadensis (Coleoptera: Pyrochroidae) larvae produce a family of antifreeze proteins (DAFPs) that are transcribed in specific tissues and have specific compartmental fates. DAFPs and associated thermal hysteresis activity (THA) have been shown previously in hemolymph and midgut fluid, but the presence of DAFPs has not been explored in primary urine, a potentially important site that can contain endogenous ice-nucleating compounds that could induce freezing. A maximum mean THA of 2.65±0.33°C was observed in primary urine of winter-collected D. canadensis larvae. THA in primary urine increased significantly through autumn, peaked in the winter and decreased through spring to levels of 0.2–0.3°C in summer, in a pattern similar to that of hemolymph and midgut fluid. THA was also found in hindgut fluid and excreted rectal fluid, suggesting that these larvae not only concentrate AFPs in the hindgut, but also excrete AFPs from the rectal cavity. Based on dafp transcripts isolated from Malpighian tubule epithelia, cDNAs were cloned and sequenced, identifying the presence of transcripts encoding 24 DAFP isoforms. Six of these Malpighian tubule DAFPs were known previously, but 18 are new. We also provide functional evidence that DAFPs can inhibit ice nucleators present in insect primary urine. This is potentially critical because D. canadensis larvae die if frozen, and therefore ice formation in any body fluid, including the urine, would be lethal

The position operator problem in periodic calculations with an emphasis on theoretical spectroscopy

In this article, we present the challenges that arise when carrying out spectroscopic simulations within periodic boundary conditions. We present approaches which were proposed in the literature for the calculation of the extension of the electric dipole moment to periodic systems. Further, we describe the challenges arising for the simulation of magnetic properties within periodic boundary conditions and for the simulation of nuclear magnetic resonance shielding tensors and related quantities. Furthermore, issues arising in periodic implementations of vibrational circular dichroism spectroscopy are described, especially for the case of atom-centered basis functions and nuclear velocity perturbation theory

Vibrational circular dichroism spectra of natural products by means of the nuclear velocity perturbation theory

We present the application of the recently implemented nuclear velocity perturbation theory, using the combined Gaussian and plane waves approach in CP2K, to the vibrational circular dichroism (VCD) spectra of a set of natural products. Even though the calculations were carried out for isolated molecules in the gas-phase limit, neglecting inter-molecular interactions and anharmonic effects, the match between simulated and experimental spectra is reasonable. We also study the influence of different density functionals on the conformational search and the resulting VCD spectra via group coupling matrices (GCMs). The GCM analysis reveals that the VCD signal can in some cases arise from moieties which are close to each other and in other cases from moieties far from each other. Differences in spectra obtained using different exchange–correlation density functionals can be attributed to interaction terms between different moieties in the molecules changing their sign

GelSight Baby Fin Ray: A Compact, Compliant, Flexible Finger with High-Resolution Tactile Sensing

The synthesis of tactile sensing with compliance is essential to many fields, from agricultural usages like fruit picking, to sustainability practices such as sorting recycling, to the creation of safe home-care robots for the elderly to age with dignity. From tactile sensing, we can discern material properties, recognize textures, and determine softness, while with compliance, we are able to securely and safely interact with the objects and the environment around us. These two abilities can culminate into a useful soft robotic gripper, such as the original GelSight Fin Ray, which is able to grasp a large variety of different objects and also perform a simple household manipulation task: wine glass reorientation. Although the original GelSight Fin Ray solves the problem of interfacing a generally rigid, high-resolution sensor with a soft, compliant structure, we can improve the robustness of the sensor and implement techniques that make such camera-based tactile sensors applicable to a wider variety of soft robot designs. We first integrate flexible mirrors and incorporate the rigid electronic components into the base of the gripper, which greatly improves the compliance of the Fin Ray structure. Then, we synthesize a flexible and high-elongation silicone adhesive-based fluorescent paint, which can provide good quality 2D tactile localization results for our sensor. Finally, we incorporate all of these techniques into a new design: the Baby Fin Ray, which we use to dig through clutter, and perform successful classification of nuts in their shells. The supplementary video can be found here: https://youtu.be/_oD_QFtYTPMComment: Accepted to IEEE Conference of Soft Robotics (RoboSoft) 202

Clinical effect of platelet rich plasma in the treatment of periodontal intrabony defects. Systematic review and meta-analysis

Introduction: One of the consequences of periodontitis is periodontal intrabony defects (PID). Various biomaterials have been used for its treatment, but there is still no biomaterial considered as the gold standard. Current research is focused on the use of platelet-rich plasma (PRP) for the treatment of PID. Objective: To determine the clinical effect of PRP in the treatment of PID through a systematic review with meta-analysis. Materials and Methods: A literature search was conducted until February 2017 in the biomedical databases: Pubmed, Embase, Scielo, Science Direct, SIGLE, LILACS, IBECS, and the Cochrane Central Register of Clinical Trials. The criteria for the selection of the studies, which were randomized clinical trials, were the following: articles or papers published in the last 5 years, reporting clinical effects, with a follow-up time equal to or greater than 6 months, and a sample size equal to or greater than 10 patients reporting the use of PRP as a treatment for PID. The methodological quality of thestudies was analyzed using the Cochrane Handbook of Systematic Reviews of Interventions as a reference. Results: The search strategy yielded nine articles reporting a reduction in probing depth and gingival recession, and an increase in clinical insertion level when using PRP alone or in combinationwith another biomaterial

The Influence of Prices on Within-Year Persistence by Traditional College-Age Students In Four-Year Colleges

This paper uses the 1987 National Postsecondary Student Aid Study to examine the influence of prices on within-year persistence by traditional college-age students enrolled in four-year colleges. The findings include: 1) within-year persistence was influenced by the amount of tuition charged; 2) tuition charges were negatively associated with within-year persistence in both public and private colleges; and 3) grant aid was positively associated with persistence in private colleges and negatively associated with persistence in public colleges. The authors conclude that the negative association between grants and persistence by students in public colleges is an artifact, attributable to an insufficient amount of grants available to students in public colleges

The Centers of Early-Type Galaxies with HST III: Non-Parametric Recovery of Stellar Luminosity Distributions

We have non-parametrically determined the luminosity density profiles and their logarithmic slopes for 42 early-type galaxies observed with HST. Assuming that the isodensity contours are spheroidal, then the luminosity density is uniquely determined from the surface brightness data through the Abel equation. For nearly all the galaxies in our sample, the logarithmic slope of the luminosity density measured at 0.1" (the innermost reliable measurement with the uncorrected HST) is significantly different from zero; i.e. most elliptical galaxies have cusps. There are only two galaxies for which an analytic core cannot be excluded. The distribution of logarithmic slopes at 0.1" appears to be bimodal, confirming the conclusion of Lauer et al. (1995) that early-type galaxies can be divided into two types based on their surface-brightness profiles; i.e., those with cuspy cores and those whose steep power-law profiles continue essentially unchanged in to the resolution limit. The peaks in the slope distribution occur at -0.8 and -1.9. More than half of the galaxies have slopes steeper than -1.0. Taken together with the recent theoretical work of Merritt & Fridman, these results suggest that many (and maybe most) elliptical galaxies are either nearly axisymmetric or spherical near the center, or slowly evolve due to the influence of stochastic orbits.Comment: uuencoded compressed tarfile 21 pages with 6 fig, 1 tabl

Effects of zooplankton size and concentration and light intensity on the feeding behavior of Atlantic mackerel \u3cem\u3eScomber scombrus\u3c/em\u3e

Atlantic mackerel Scomber scombrus had low clearance rates when fed older stage copepodites of the copepod Calanus finmarchicus at high concentrations and high clearance rates at low concentrations. These rates were consistent with filter feeding at high concentrations and particulate feeding at low concentrations. Intermediate and small copepods presented together at high concentrations were cleared at lower rates than the large C. finmarchicus, suggesting lower filtration efficiencies. Intermediate and small copepods were presented over a range of light intensities (8.2 x 10-8 to 1.6 x 100 µE m-2 s-1). Feeding rate did not change significantly between 1.6 x 100 and 2.0 x 10-6 µE m-2 s-1, but decreased to nearly zero at 8.2 x 10-8 µE m-2 s-1, indicating a light intensity threshold for feeding of about 10-7 µE m-2 s-1. This threshold enables mackerel to feed throughout the night near the ocean surface. Swimming speed decreased to a lesser degree than feeding rate at the lowest light intensity, indicating that the change in filter-feeding rate is only partially due to the change in speed. The school dispersed in both low and high light levels, but spacing between fish did not appear to be related to feeding rate