Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

Journal of Computer-Aided Molecular Design - We report the performance of our newly introduced Ensemble Docking with Enhanced sampling of pocket Shape (EDES) protocol coupled to a template-based...     

A quantum mechanical explanation of the structure of vinyl cation based on a CASSCF/CASMP2 study

An ab-initio CASSCF/CASMP2 study on the structures and energies of the classical and bridged forms of the vinyl cation is presented. Our calculations which are in agreement with the experimental results predict that the bridged form of the vinyl cation (C₂H₃ ⁺) is more stable than its classical counterpart and is the unique species on the potential energy surface. A quantum mechanical explanation based in the notion of electron correlation energy and in Boltzmann distribution shows that the classical form is considered to be a transient species having a fleeting existence.     

Motion of Drops with Different Viscosities on Micro‐Nanotextured Surfaces of Varying Topography and Wetting Properties

Superhydrophobic surfaces are extensively investigated in the literature, yet the phenomenon of drop motion on such surfaces and the corresponding friction properties of surfaces with different topography are not sufficiently analyzed. Here, drop motion on hydrophobic and superhydrophobic surfaces with different size topography is investigated for drops of largely varying viscosity (i.e., water and glycerol). The threshold force required to initiate drop movement is probed, the drop motion (velocity and acceleration) is analyzed, and the friction force on each surface is calculated. It is evident that as roughness increases, the threshold force to initiate 20 µL drop motion decreases; the lowest value for water is 17.9 ± 4.0 µN. For glycerol, the lowest threshold force value is 22.3 ± 5.9 µN. The results also indicate that this threshold force required for the initiation of the drop motion seems to be higher than that when the drop starts moving. Finally, this force (being proportional to the contact line) is expected to be about half smaller for 5 µL droplets. Water drops obtain higher velocities and accelerations by an order of magnitude compared to glycerol drops, which is attributed to the combinational effect of the higher hysteresis and the larger contact line of glycerol drops.     

Joint multi-cost routing and power control in wireless ad hoc networks

In this work we study the combination of multi-cost routing and adjustable transmission power in wireless ad hoc networks, so as to obtain dynamic energy- and interference-efficient routes to optimize network performance. In multi-cost routing, a vector of cost parameters is assigned to each network link, from which the cost vectors of candidate paths are calculated. Only at the end these parameters are combined in various optimization functions, corresponding to different routing algorithms, for selecting the optimal path. The multi-cost routing problem is a generalization of the multi-constrained problem, where no constraints exist, and is also significantly more powerful than single-cost routing. Since energy is an important limitation of wireless communications, the cost parameters considered are the number of hops, the interference caused, the residual energy and the transmission power of the nodes on the path; other parameters could also be included, as desired. We assume that nodes can use power control to adjust their transmission power to the desired level. The experiments conducted show that the combination of multi-cost routing and adjustable transmission power can lead to reduced interference and energy consumption, improving network performance and lifetime.     

Enhancing Channel Estimation in Cognitive Radio Systems by means of Bayesian Networks

This paper proposes enhancements to the channel(-state) estimation phase of a cognitive radio system. Cognitive radio devices have the ability to dynamically select their operating configurations, based on environment aspects, goals, profiles, preferences etc. The proposed method aims at evaluating the various candidate configurations that a cognitive transmitter may operate in, by associating a capability e.g., achievable bit-rate, with each of these configurations. It takes into account calculations of channel capacity provided by channel-state estimation information (CSI) and the sensed environment, and at the same time increases the certainty about the configuration evaluations by considering past experience and knowledge through the use of Bayesian networks. Results from comprehensive scenarios show the impact of our method on the behaviour of cognitive radio systems, whereas potential application and future work are identified.

Emerging,Self-Management Functionality for Introducing Cognition in the Wireless,B3G World

The unparalleled evolution of wireless communications is reflected in the tremendous investments on research and development, targeted at the continuous introduction of innovations that could serve the information society. This has led to the coexistence and complementary exploitation of versatile, legacy and also emerging Radio Access Technologies (RATs). At the same time, the continuously varying environment/users requirements impose the adaptation of those technologies to external stimuli, through reconfiguration (reconsideration) of their infrastructure and/or operating parameters. One feasible option to tackle the increased complexity of such environments, is to design wireless infrastructures with learning capabilities, thus forming cognitive networks. Cognitive networks are able to retain information from their interactions with the environment and intelligently adapt to any requirements. A prerequisite to facilitate operability of cognitive networks is the development of novel management mechanisms, which need to, distributively (centralized approaches would get even more complex), evaluate changes in external conditions and determine the way in which the network will properly respond to them. To this effect, this paper presents a complete framework under which Cognitive Access Points (CgAPs) could be managed and analyzes the functionality of its entities. Moreover, it also provides an approach for managing Cognitive Wireless Network Segments (CgWNSs).

The Stochastic Quasi-chemical Model for Bacterial Growth: Variational Bayesian Parameter Update

We develop Bayesian methodologies for constructing and estimating a stochastic quasi-chemical model (QCM) for bacterial growth. The deterministic QCM, described as a nonlinear system of ODEs, is treated as a dynamical system with random parameters, and a variational approach is used to approximate their probability distributions and explore the propagation of uncertainty through the model. The approach consists of approximating the parameters’ posterior distribution by a probability measure chosen from a parametric family, through minimization of their Kullback–Leibler divergence.     

On the security of the Feng–Liao–Yang Boolean functions with optimal algebraic immunity against fast algebraic attacks

In the past few years, algebraic attacks against stream ciphers with linear feedback function have been significantly improved. As a response to the new attacks, the notion of algebraic immunity of a Boolean function f was introduced, defined as the minimum degree of the annihilators of f and f + 1. An annihilator of f is a nonzero Boolean function g, such that fg = 0. There is an increasing interest in construction of Boolean functions that possess optimal algebraic immunity, combined with other characteristics, like balancedness, high nonlinearity, and high algebraic degree. In this paper, we investigate a recently proposed infinite class of balanced Boolean functions with optimal algebraic immunity, optimum algebraic degree and much better nonlinearity than all the previously introduced classes of Boolean functions with maximal algebraic immunity. More precisely, we study the resistance of the functions against one of the new algebraic attacks, namely the fast algebraic attacks (FAAs). Using the special characteristics of the family members, we introduce an efficient method for the evaluation of their behavior against these attacks. The new algorithm is based on the well studied Berlekamp–Massey algorithm.