DNA and its counterions: A molecular dynamics study

The behaviour of mobile counterions, Na+ and K+, was analysed around a B-DNA double helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long molecular dynamics trajectories. The movement of both monovalent ions remains diffusive in the presence of DNA. Ions sample the complete space available during the simulation time, although individual ions sample only about one-third of the simulation box. Ions preferentially sample electronegative sites around DNA, but direct binding to DNA bases remains a rather rare event, with highest site occupancy values of <13%. The location of direct binding sites depends greatly on the nature of the counterion. While Na+ binding in both grooves is strongly sequence-dependent with the preferred binding site in the minor groove, K+ mainly visits the major groove and binds close to the centre of the oligomer. The electrostatic potential of an average DNA structure therefore cannot account for the ability of a site to bind a given cation; other factors must also play a role. An extensive analysis of the influence of counterions on DNA conformation showed no evidence of minor groove narrowing upon ion binding. A significant difference between the conformations of the double helix in the different simulations can be attributed to extensive (/ transitions in the phosphate backbone during the simulation with Na+. These transitions, with lifetimes over tens of nanoseconds, however, appear to be correlated with ion binding to phosphates. The ion-specific conformational properties of DNA, hitherto largely overlooked, may play an important role in DNA recognition and binding

Differential stability of DNA crossovers in solution mediated by divalent cations

The assembly of DNA duplexes into higher-order structures plays a major role in many vital cellular functions such as recombination, chromatin packaging and gene regulation. However, little is currently known about the molecular structure and stability of direct DNADNA interactions that are required for such functions. In nature, DNA helices minimize electrostatic repulsion between double helices in several ways. Within crystals, B-DNA forms either right-handed crossovers by groovebackbone interaction or left-handed crossovers by groovegroove juxtaposition. We evaluated the stability of such crossovers at various ionic concentrations using large-scale atomistic molecular dynamics simulations. Our results show that right-handed DNA crossovers are thermodynamically stable in solution in the presence of divalent cations. Attractive forces at short-range stabilize such crossover structures with inter-axial separation of helices less than 20 . Right-handed crossovers, however, dissociate swiftly in the presence of monovalent ions only. Surprisingly, left-handed crossovers, assembled by sequence-independent juxtaposition of the helices, appear unstable even at the highest concentration of Mg2+studied here. Our study provides new molecular insights into chiral association of DNA duplexes and highlights the unique role divalent cations play in differential stabilization of crossover structures. These results may serve as a rational basis to understand the role DNA crossovers play in biological processes

Package Hermeticity Testing with Thermal Transient Measurements

The rapid incursion of new technologies such as MEMS and smart sensor device manufacturing requires new tailor-made packaging designs. In many applications these devices are exposed to humid environments. Since the penetration of moisture into the package may result in internal corrosion or shift of the operating parameters, the reliability testing of hermetically sealed packages has become a crucial question in the semiconductor industry.Comment: Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/16838

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.

The conformational pathways and the free energy variations for base opening into the major and minor grooves of a B-DNA duplex are studied using umbrella sampling molecular dynamics simulations. We compare both GC and AT base pair opening within a double-stranded d(GAGAGAGAGAGAG). d(CTCTCTCTCTCTC) oligomer, and we are also able to study the impact of opening on the conformational and dynamic properties of DNA and on the surrounding solvent. The results indicate a two-stage opening process with an initial coupling of the movements of the bases within the perturbed base pair. Major and minor groove pathways are energetically comparable in the case of the pyrimidine bases, but the major groove pathway is favored for the larger purine bases. Base opening is coupled to changes in specific backbone dihedrals and certain helical distortions, including untwisting and bending, although all these effects are dependent on the particular base involved. Partial opening also leads to well defined water bridging sites, which may play a role in stabilizing the perturbed base pairs

Prescribed Performance Control Guided Policy Improvement for Satisfying Signal Temporal Logic Tasks

Signal temporal logic (STL) provides a user-friendly interface for defining complex tasks for robotic systems. Recent efforts aim at designing control laws or using reinforcement learning methods to find policies which guarantee satisfaction of these tasks. While the former suffer from the trade-off between task specification and computational complexity, the latter encounter difficulties in exploration as the tasks become more complex and challenging to satisfy. This paper proposes to combine the benefits of the two approaches and use an efficient prescribed performance control (PPC) base law to guide exploration within the reinforcement learning algorithm. The potential of the method is demonstrated in a simulated environment through two sample navigational tasks.Comment: This is the extended version of the paper accepted to the 2019 American Control Conference (ACC), Philadelphia (to be published

EPIC spectral observations of variability in earth’s global reflectance

NASA's Earth Polychromatic Imaging Camera (EPIC) onboard NOAA's Deep Space Climate Observatory (DSCOVR) satellite observes the entire sunlit Earth every 65 to 110 min from the Sun-Earth Lagrangian L1 point. This paper presents initial EPIC shortwave spectral observations of the sunlit Earth reflectance and analyses of its diurnal and seasonal variations. The results show that the reflectance depends mostly on (1) the ratio between land and ocean areas exposed to the Sun and (2) cloud spatial and temporal distributions over the sunlit side of Earth. In particular, the paper shows that (a) diurnal variations of the Earth's reflectance are determined mostly by periodic changes in the land-ocean fraction of its the sunlit side; (b) the daily reflectance displays clear seasonal variations that are significant even without including the contributions from snow and ice in the polar regions (which can enhance daily mean reflectances by up to 2 to 6% in winter and up to 1 to 4% in summer); (c) the seasonal variations of the sunlit Earth reflectance are mostly determined by the latitudinal distribution of oceanic clouds

Multiyear Statistics of 2-D Shortwave Radiative Effects at Three ARM Sites

This study examines the importance of horizontal photon transport effects, which are not considered in the 1-D calculations of solar radiative heating used by most atmospheric dynamical models. In particular, the paper analyzes the difference between 2-D and 1-D radiative calculations for 2-D vertical cross-sections of clouds that were observed at three sites over 2- to 3-year periods. The results show that 2-D effects increase multiyear 24-hour average total solar absorption by about 4.1 W/sq m, 1.2 W/sq m, and 0.3 W/sq m at a tropical, mid-latitude, and arctic site, respectively. However, 2-D effects are often much larger than these average values, especially for high sun and for convective clouds. The results also reveal a somewhat unexpected behavior, that horizontal photon transport often enhances solar heating even for oblique sun. These findings underscore the need for fast radiation calculation methods that can allow atmospheric dynamical simulations to consider the inherently multidimensional nature of shortwave radiative processes

Porous Alumina Based Capacitive MEMS RH Sensor

The aim of a joint research and development project at the BME and HWU is to produce a cheap, reliable, low-power and CMOS-MEMS process compatible capacitive type relative humidity (RH) sensor that can be incorporated into a state-of-the-art, wireless sensor network. In this paper we discuss the preparation of our new capacitive structure based on post-CMOS MEMS processes and the methods which were used to characterize the thin film porous alumina sensing layer. The average sensitivity is approx. 15 pF/RH% which is more than a magnitude higher than the values found in the literature. The sensor is equipped with integrated resistive heating, which can be used for maintenance to reduce drift, or for keeping the sensing layer at elevated temperature, as an alternative method for temperature-dependence cancellation.Comment: Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/16838

Effect of Cloud Fraction on Near-Cloud Aerosol Behavior in the MODIS Atmospheric Correction Ocean Color Product

Characterizing the way satellite-based aerosol statistics change near clouds is important for better understanding both aerosol-cloud interactions and aerosol direct radiative forcing. This study focuses on the question of whether the observed near-cloud increases in aerosol optical thickness and particle size may be explained by a combination of two factors: (i) Near-cloud data coming from areas with higher cloud fractions than far-from-cloud data and (ii) Cloud fraction being correlated with aerosol optical thickness and particle size. This question is addressed through a statistical analysis of aerosol parameters included in the MODIS (MODerate resolution Imaging Spectroradiometer) ocean color product. Results from ten Septembers (2002-2011) over part of the northeast Atlantic Ocean confirm that the combination of these two factors working together explains a significant but not dominant part (in our case, 15%-30%) of mean optical thickness changes near clouds. Overall, the findings show that cloud fraction plays a large role in shaping the way aerosol statistics change with distance to clouds. This implies that both cloud fraction and distance to clouds are important to consider when aerosol-cloud interactions or aerosol direct radiative effects are examined in satellite or modeling studies