The resonance raman spectrum of cytosine in water: analysis of the effect of specific solute–solvent interactions and non-adiabatic couplings

In this contribution, we report a computational study of the vibrational Resonance Raman (vRR) spectra of cytosine in water, on the grounds of potential energy surfaces (PES) computed by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. Cytosine is interesting because it is characterized by several close-lying and coupled electronic states, challenging the approach commonly used to compute the vRR for systems where the excitation frequency is in quasi-resonance with a single state. We adopt two recently developed time-dependent approaches, based either on quantum dynamical numerical propagations of vibronic wavepackets on coupled PES or on analytical correlation functions for cases in which inter-state couplings were neglected. In this way, we compute the vRR spectra, considering the quasi-resonance with the eight lowest-energy excited states, disentangling the role of their inter-state couplings from the mere interference of their different contributions to the transition polarizability. We show that these effects are only moderate in the excitation energy range explored by experiments, where the spectral patterns can be rationalized from the simple analysis of displacements of the equilibrium positions along the different states. Conversely, at higher energies, interference and inter-state couplings play a major role, and the adoption of a fully non-adiabatic approach is strongly recommended. We also investigate the effect of specific solute–solvent interactions on the vRR spectra, by considering a cluster of cytosine, hydrogen-bonded by six water molecules, and embedded in a polarizable continuum. We show that their inclusion remarkably improves the agreement with the experiments, mainly altering the composition of the normal modes, in terms of internal valence coordinates. We also document cases, mostly for low-frequency modes, in which a cluster model is not sufficient, and more elaborate mixed quantum classical approaches, in explicit solvent models, need to be applie

On Transient Response of Piezoelectric Transducers

In this paper, we report a new model in analysis of spherical thin-shell piezoelectric transducers for transient response, based on Fourier transform and the principle of linear superposition. We show that a circuit-network, a combination of a series of parallel-connected equivalent-circuits, can be used in description of a spherical thin-shell piezoelectric transducer. When excited by a signal with multiple frequency components, each circuit would have a distinctive radiation resistance and a radiation mass, arising from an individual frequency component. Each frequency component would act independently on the electric/mechanic-terminals. A cumulative signal-output from the mechanic/electric-terminals is measured as the overall acoustic/electric output. As a prototype example in testing the new model, we have designed two spherical shin-shell transducers, applied a gated sine electric-signal as the initial excitation, and recorded the experimental information. The transient response and the output signals are calculated based on the new model. The results of calculation are in good agreement with that of experimental observation

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Sarcopenia; Aging-related loss of muscle mass and function

Sarcopenia is a loss of muscle mass and function in the elderly that reduces mobility, diminishes quality of life, and can lead to fall-related injuries, which require costly hospitalization and extended rehabilitation. This review focuses on the aging-related structural changes and mechanisms at cellular and subcellular levels underlying changes in the individual motor unit: specifically, the perikaryon of -motoneuron, its neuromuscular junction(s), and the muscle fibers that it innervates. Loss of muscle mass with aging, which is largely due to the progressive loss of motoneurons, is associated with reduced muscle fiber number and size. Muscle function progressively declines because motoneuron loss is not adequately compensated by reinnervation of muscle fibers by the remaining motoneurons. At the intracellular level, key factors are qualitative changes in posttranslational modifications of muscle proteins and the loss of coordinated control between contractile, mitochondrial, and sarcoplasmic reticulum protein expression. Quantitative and qualitative changes in skeletal muscle during the process of aging also have been implicated in the pathogenesis of acquired and hereditary neuromuscular disorders. In experimental models, specific intervention strategies have shown encouraging results on limiting deterioration of motor unit structure and function under conditions of impaired innervation. Translated to the clinic, if these or similar interventions, by saving muscle and improving mobility, could help alleviate sarcopenia in the elderly, there would be both great humanitarian benefits and large cost savings for health care systems

Impurity Controlled near Infrared Surface Plasmonic in AlN

In this work, we used multi-scale computational simulation methods combined with density functional theory (DFT) and finite element analysis (FEA) in order to study the optical properties of substitutional doped aluminium nitride (AlN). There was strong surface plasmon resonance (SPR) in the near-infrared region of AlN substituted with different alkali metal doping configurations. The strongest electric field strength reached 109 V/m. There were local exciton and charge transfer exciton behaviours in some special doping configurations. These research results not only improve the application of multi-scale computational simulations in quantum surface plasmons, but also promote the application of AlN in the field of surface-enhanced linear and non-linear optical spectroscopy

Influence of Vacancy Defect on Surface Feature and Adsorption of Cs on GaN(0001) Surface

The effects of Ga and N vacancy defect on the change in surface feature, work function, and characteristic of Cs adsorption on a 2×2 GaN(0001) surface have been investigated using density functional theory with a plane-wave ultrasoft pseudopotential method based on first-principles calculations. The covalent bonds gain strength for Ga vacancy defect, whereas they grow weak for N vacancy defect. The lower work function is achieved for Ga and N vacancy defect surfaces than intact surface. The most stable position of Cs adatom on Ga vacancy defect surface is at T1 site, whereas it is at BGa site on N vacancy defect surface. The Eads of Cs on GaN(0001) vacancy defect surface increases compared with that of intact surface; this illustrates that the adsorption of Cs on intact surface is more stable