Molecular dynamics of nanodroplet impact: The effect of the projectile’s molecular mass on sputtering

The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated

CplexA: a Mathematica package to study macromolecular-assembly control of gene expression

Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions. The package is particularly suited to study gene expression at complex promoters controlled by multiple, local and distal, DNA binding sites for transcription factors. Availability: CplexA is freely available together with documentation at http://sourceforge.net/projects/cplexa/.Comment: 28 pages. Includes Mathematica, Matlab, and Python implementation tutorials. Software can be downloaded at http://cplexa.sourceforge.net

Interactions and thermoelectric effects in a parallel-coupled double quantum dot

We investigate the nonequilibrium transport properties of a double quantum dot system connected in parallel to two leads, including intradot electron-electron interaction. In the absence of interactions the system supports a bound state in the continuum. This state is revealed as a Fano antiresonance in the transmission when the energy levels of the dots are detuned. Using the Keldysh nonequilibrium Green's function formalism, we find that the occurrence of the Fano antiresonance survives in the presence of Coulomb repulsion. We give precise predictions for the experimental detection of bound states in the continuum. First, we calculate the differential conductance as a function of the applied voltage and the dot level detuning and find that crossing points in the diamond structure are revealed as minima due to the transmission antiresonances. Second, we determine the thermoelectric current in response to an applied temperature bias. In the linear regime, quantum interference gives rise to sharp peaks in the thermoelectric conductance. Remarkably, we find interaction induced strong current nonlinearities for large thermal gradients that may lead to several nontrivial zeros in the thermocurrent. The latter property is especially attractive for thermoelectric applications.Comment: 9 pages, 8 figure

Stochastic dynamics of macromolecular-assembly networks

The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage lambda induction switches, which rely on the formation of DNA loops by proteins and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes.Comment: Open Access article available at http://www.nature.com/msb/journal/v2/n1/full/msb4100061.htm

Multiprotein DNA looping

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.Comment: 11 pages, 4 figure

Enhancing thermoelectric properties of graphene quantum rings

We study the thermoelectric properties of rectangular graphene rings connected symmetrically or asymmetrically to the leads. A side-gate voltage applied across the ring allows for the precise control of the electric current flowing through the system. The transmission coefficient of the rings manifests Breit-Wigner line-shapes and/or Fano line-shapes, depending on the connection configuration, the width of nanoribbons forming the ring and the side-gate voltage. We find that the thermopower and the figure of merit are greatly enhanced when the chemical potential is tuned close to resonances. Such enhancement is even more pronounced in the vicinity of Fano like anti-resonances which can be induced by a side-gate voltage independently of the geometry. This opens a possibility to use the proposed device as a tunable thermoelectric generator.Comment: 6 pages, 5 figures, accepted for publication in Physical Review

Lattice thermal conductivity of graphene nanostructures

Non-equilibrium molecular dynamics is used to investigate the heat current due to the atomic lattice vibrations in graphene nanoribbons and nanorings under a thermal gradient. We consider a wide range of temperature, nanoribbon widths up to 6nm and the effect of moderate edge disorder. We find that narrow graphene nanorings can efficiently suppress the lattice thermal conductivity at low temperatures (~100K), as compared to nanoribbons of the same width. Remarkably, rough edges do not appear to have a large impact on lattice energy transport through graphene nanorings while nanoribbons seem more affected by imperfections. Furthermore, we demonstrate that the effects of hydrogen-saturated edges can be neglected in these graphene nanostructures

Computational modeling of the auditory brainstem response to continuous speech.

OBJECTIVE: The auditory brainstem response can be recorded non-invasively from scalp electrodes and serves as an important clinical measure of hearing function. We have recently shown how the brainstem response at the fundamental frequency of continuous, non-repetitive speech can be measured, and have used this measure to demonstrate that the response is modulated by selective attention. However, different parts of the speech signal as well as several parts of the brainstem contribute to this response. Here we employ a computational model of the brainstem to elucidate the influence of these different factors. APPROACH: We developed a computational model of the auditory brainstem by combining a model of the middle and inner ear with a model of globular bushy cells in the cochlear nuclei and with a phenomenological model of the inferior colliculus. We then employed the model to investigate the neural response to continuous speech at different stages in the brainstem, following the methodology developed recently by ourselves for detecting the brainstem response to running speech from scalp recordings. We compared the simulations with recordings from healthy volunteers. MAIN RESULTS: We found that the auditory-nerve fibers, the cochlear nuclei and the inferior colliculus all contributed to the speech-evoked brainstem response, although the dominant contribution came from the inferior colliculus. The delay of the response corresponded to that observed in experiments. We further found that a broad range of harmonics of the fundamental frequency, up to about 8 kHz, contributed to the brainstem response. The response declined with increasing fundamental frequency, although the signal-to-noise ratio was largely unaffected. SIGNIFICANCE: Our results suggest that the scalp-recorded brainstem response at the fundamental frequency of speech originates predominantly in the inferior colliculus. They further show that the response is shaped by a large number of higher harmonics of the fundamental frequency, reflecting highly nonlinear processing in the auditory periphery and illustrating the complexity of the response

Short Communication. Physiological effects of Rhizopogon Roseolus on Pinus halepensis seedlings

Aim of study: The inoculation of forest seedlings with ectomycorrhizal fungi can improve the morphological and physiological qualities of plants, especially those used for regeneration of arid areas. Rhizopogon roseolus is an ectomycorrhizal fungus (ECM) commonly used for reforestation. In this study, the specific objectives were to know some morphophysiological effects of Rhizopogon Roseolus on Pinus halepensis seedlings under standard nursery conditionsArea of study: ETSI Montes and EUIT Forestal, Madrid.Material and Methods: In nursery, under well watered conditions and peat growing substrates, Aleppo pine seedlings were inoculated with R. roseolus. Five months after the inoculations, we examined the growth, water parameters (osmotic potential at full turgor [Ψπfull], osmotic potential at zero turgor [Ψπ0], and the tissue modulus of elasticity near full turgor [Emax]), mycorrhizal colonization, and concentration and content of macronutrients in the seedlings. Subsequently, a trial was conducted to assess the root growth potential.Main results: The mycorrhization decreased the height and diameter of mycorrhizal seedlings but increased the root weight and root branching. R. roseolus did not cause any significant effect on the regeneration of new roots or on any of the tested hydric parameters, but it did improve N uptake of the seedlings.Research highlights: The mycorrhizal inoculation increased the N uptake. The mycorrhizal inoculation caused opposite effects on some growth parametersKeywords: Osmotic adjustment; elastic adjustment; mineral nutrition; root growth potential; nursery; Rhizopogon roseolus;  Pinus halepensis.