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Amphid wing “C” (AWC) neurons are among the most important and studied neurons of the nematode Caenorhabditis elegans. In this work, we unify the existing electrical and intracellular calcium dynamics descriptions to obtain a biophysically accurate model of olfactory transduction in AWCON neurons. We study the membrane voltage and the intracellular calcium dynamics at different exposure times and odorant concentrations to grasp a complete picture of AWCON functioning. Moreover, we investigate the complex cascade of biochemical processes that allow AWC activation upon odor removal. We analyze the behavior of the different components of the models and, by suppressing them selectively, we extrapolate their contribution to the overall neuron response and study the resilience of the dynamical system. Our results are all in agreement with the available experimental data. Therefore, we provide an accurate mathematical and biophysical model for studying olfactory signal processing in C. elegans.

Nonuniform density scaling in the quasi-two-dimensional (quasi-2D) regime is an important and challenging aspect of the density functional theory. Semilocal exchange-correlation energy functionals, developed by solving the dimensional crossover criterion in the quasi-2D regime, have great theoretical and practical importance. However, the only semilocal generalized gradient approximation (GGA) that has been designed to satisfy this criterion is the Q2D-GGA [L. Chiodo et al., Phys. Rev. Lett. 108, 126402 (2012)]. Here, we establish the applicability, broadness, and accuracy of the Q2D-GGA functional by performing an extensive assessment of this functional for transition metal surface energies. The important characteristic of the surface density localization and oscillation due to the rearrangement of the d electrons is also shown for different metal surfaces. [ABSTRACT FROM AUTHOR]

Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be determined by experimental means. Starting from β‐rich aggregates of Y and elongated topologies predicted by coarse‐grained simulations and consisting of more than 100 Aβ16–22 peptides, we performed atomistic molecular dynamics (MD), replica exchange with solute scaling (REST2), and umbrella sampling simulations using the CHARMM36m force field in explicit solvent. Here, we explored the dynamics within 3 μs, the free energy landscape, and the potential of mean force associated with either the unbinding of one single peptide in different configurations within the aggregate or fragmentation events of a large number of peptides. Within the time scale of MD and REST2, we find that the aggregates experience slow global conformational plasticity, and remain essentially random coil though we observe slow beta‐strand structuring with a dominance of antiparallel beta‐sheets over parallel beta‐sheets. Enhanced REST2 simulation is able to capture fragmentation events, and the free energy of fragmentation of a large block of peptides is found to be similar to the free energy associated with fibril depolymerization by one chain for longer Aβ sequences. [ABSTRACT FROM AUTHOR]

AWC olfactory neurons are fundamental for chemotaxis toward volatile attractants in Caenorhabditis elegans. Here, it is shown that AWCON responds not only to chemicals but also to mechanical stimuli caused by fluid flow changes in a microfluidic device. The dynamics of calcium events are correlated with the stimulus amplitude. It is further shown that the mechanosensitivity of AWCON neurons has an intrinsic nature rather than a synaptic origin, and the calcium transient response is mediated by TAX‐4 cGMP‐gated cation channel, suggesting the involvement of one or more "odorant" receptors in AWCON mechano‐transduction. In many cases, the responses show plateau properties resembling bistable calcium dynamics where neurons can switch from one stable state to the other. To investigate the unprecedentedly observed mechanosensitivity of AWCON neurons, a novel microfluidic device is designed to minimize the fluid shear flow in the arena hosting the nematodes. Animals in this device show reduced neuronal activation of AWCON neurons. The results observed indicate that the tangential component of the mechanical stress is the main contributor to the mechanosensitivity of AWCON. Furthermore, the microfluidic platform, integrating shearless perfusion and calcium imaging, provides a novel and more controlled solution for in vivo analysis both in micro‐organisms and cultured cells. [ABSTRACT FROM AUTHOR]

A monolayer of bismuth deposited on the Cu(100) surface forms a highly ordered c(2×2) reconstructed phase. The low energy single particle excitations of the c(2×2) Bi/Cu(100) present Bi-induced states with a parabolic dispersion in the energy region close to the Fermi level, as observed by angle-resolved photoemission spectroscopy. The electronic state dispersion, the charge density localization, and the spin-orbit coupling have been investigated combining photoemission spectroscopy and density functional theory, unraveling a two-dimensional Bi phase with charge density well localized at the interface. The Bi-induced states present a Rashba splitting, when the charge density is strongly localized in the Bi plane. Furthermore, the temperature dependence of the spectral density close to the Fermi level has been evaluated. Dispersive electronic states offer a large number of decay channels for transitions coupled to phonons and the strength of the electron-phonon coupling for the Bi/Cu(100) system is shown to be stronger than for Bi surfaces and to depend on the electronic state symmetry and localization. [ABSTRACT FROM AUTHOR]

Atomic clusters of TiO2 are modeled by means of state-of-the-art techniques to characterize their structural, electronic and optical properties. We combine ab initio molecular dynamics, static density functional theory, time-dependent density functional theory, and many body techniques, to provide a deep and comprehensive characterization of these systems. TiO2 clusters can be considered as the starting seeds for the synthesis of larger nanostructures, which are of technological interest in photocatalysis and photovoltaics. In this work, we prove that clusters with anatase symmetry are energetically stable and can be considered as the starting seeds to growth much larger and complex nanostructures. The electronic gap of these inorganic molecules is investigated, and shown to be larger than the optical gap by almost 4 eV. Therefore, strong excitonic effects appear in these systems, much more than in the corresponding bulk phase. Moreover, the use of various levels of theory demonstrates that charge transfer effects play an important role under photon absorption, and therefore the use of adiabatic functionals in time dependent density functional theory has to be carefully evaluated. [ABSTRACT FROM AUTHOR]

The dihydrogen complex Ru(H2)2H2(P(C5H9)3)2 has been investigated, via ab initio accelerated molecular dynamics, to elucidate the H ligands dynamics and possible reaction paths for H2/H exchange. We have characterized the free energy landscape associated with the H atoms positional exchange around the Ru centre. From the free energy landscape, we have been able to estimate a barrier of 6 kcal mol−1 for the H2/H exchange process. We have also observed a trihydrogen intermediate as a passing state along some of the possible reaction pathways. [ABSTRACT FROM AUTHOR]

C. elegans neuronal system constitutes the ideal framework for studying simple, yet realistic, neuronal activity, since the whole nervous system is fully characterized with respect to the exact number of neurons and the neuronal connections. Most recent efforts are devoted to investigate and clarify the signal processing and functional connectivity, which are at the basis of sensing mechanisms, signal transmission, and motor control. In this framework, a refined modelof whole neuron dynamics constitutes a key ingredient to describe the electrophysiological processes, both at thecellular and at the network scale. In this work, we present Hodgkin-Huxley-based models of ion channels dynamics black, built on data available both from C. elegans and from other organisms, expressing homologous channels. We combine these channel models to simulate the electrical activity oftwo among the most studied neurons in C. elegans, which display prototypical dynamics of neuronal activation, the chemosensory AWCON and the motor neuron RMD. Our model properly describes the regenerative responses of the two cells. We analyze in detail the role of ion currents, both in wild type and in in silico knockout neurons. Moreover, we specifically investigate the behavior of RMD, identifying a heterogeneous dynamical response which includes bistable regimes and sustained oscillations. We are able to assess the critical role of T-type calcium currents, carried by CCA-1 channels, and leakage currents in the regulation of RMD response. Overall, our results provide new insights in the activity of key C. elegans neurons. The developed mathematical framework constitute a basis for single-cell and neuronal networks analyses, opening new scenarios in the in silico modeling of C. elegans neuronal system. [ABSTRACT FROM AUTHOR]