Investigating viral protein U (Vpu) of HIV-1 using all-atom molecular dynamics

Viral Protein U (Vpu) is an accessory protein of the HIV-1 virus and a member of the Viral Channel Forming protein (VCP) family. A HIV-1 virus with Vpu is 10 times more infectious than a Vpu deficient HIV-1 virus. Vpu consists of 81 amino acids, with one transmembrane (TM) helix close to the N-terminus and two cytoplasmic (Cyto) helices. It is involved in more than ten different activities. The most well studied functions are CD4 degradation and BST2 antagonism. Vpu also forms an ion channel. However, its functions, structure, and mechanisms currently remain unclear. This research focuses on looking for a better insight into Vpu-mediated channel activity. Computational simulations using Molecular Dynamics (MD) have provided a way to overcome the experimental limitations. AMBER is a MD package to simulate biological systems at an atomistic level of detail. Its lipid force-field, Lipid 14 (recently updated to lipid 17, unpublished) contains a range of parameters for lipid head and tail groups separately, enabling a variety of lipids to be simulated by mix-and-match different head and tail combinations. Nowadays, much longer and more accurate computational simulations can be achieved. This project has first evaluated the lipid force-field, and developed a systematic methodology to perform all-atom membrane-protein simulations. The key biological finding is that a single full-length Vpu monomer can support a pore, as opposed to the necessity for a Vpu oligomer, as has previously been suggested. The results indicate that a variety of Vpu oligomers co-exist, resulting in a range of pores with various sizes. The pores observed at higher oligomeric states are closer to a ring-like structure. The transportation of substances (K+, Cl- and POPS) across the membrane is facilitated by the Vpu-mediated pore. A cationic selectivity is observed in the spontaneous ion translocation, which is confirmed using potential-of-mean-force (PMF) simulations.Open Acces

Memristive Perceptron for Combinational Logic Classification

The resistance of the memristor depends upon the past history of the input current or voltage; so it can function as synapse in neural networks. In this paper, a novel perceptron combined with the memristor is proposed to implement the combinational logic classification. The relationship between the memristive conductance change and the synapse weight update is deduced, and the memristive perceptron model and its synaptic weight update rule are explored. The feasibility of the novel memristive perceptron for implementing the combinational logic classification (NAND, NOR, XOR, and NXOR) is confirmed by MATLAB simulation

On the number of frequency hypercubes Fn(4;2,2)F^n(4;2,2)

A frequency $n$-cube $F^n(4;2,2)$ is an $n$-dimensional $4\times\cdots\times 4$ array filled by $0$s and $1$s such that each line contains exactly two $1$s. We classify the frequency $4$-cubes $F^4(4;2,2)$, find a testing set of size $25$ for $F^3(4;2,2)$, and derive an upper bound on the number of $F^n(4;2,2)$. Additionally, for any $n$ greater than $2$, we construct an $F^n(4;2,2)$ that cannot be refined to a latin hypercube, while each of its sub-$F^{n-1}(4;2,2)$ can. Keywords: frequency hypercube, frequency square, latin hypercube, testing set, MDS cod

Self-orthogonal codes over a non-unital ring and combinatorial matrices

There is a local ring $E$ of order $4,$ without identity for the multiplication, defined by generators and relations as $E=\langle a,b \mid 2a=2b=0,\, a^2=a,\, b^2=b,\,ab=a,\, ba=b\rangle.$ We study a special construction of self-orthogonal codes over $E,$ based on combinatorial matrices related to two-class association schemes, Strongly Regular Graphs (SRG), and Doubly Regular Tournaments (DRT). We construct quasi self-dual codes over $E,$ and Type IV codes, that is, quasi self-dual codes whose all codewords have even Hamming weight. All these codes can be represented as formally self-dual additive codes over \F_4. The classical invariant theory bound for the weight enumerators of this class of codesimproves the known bound on the minimum distance of Type IV codes over $E.$Comment: 18 page

A Chaotic Attractor in Delayed Memristive System

Over the last three decades, theoretical design and circuitry implementation of various chaotic generators by simple electronic circuits have been a key subject of nonlinear science. In 2008, the successful development of memristor brings new activity for this research. Memristor is a new nanometre-scale passive circuit element, which possesses memory and nonlinear characteristics. This makes it have a unique charm to attract many researchers’ interests. In this paper, memristor, for the first time, is introduced in a delayed system to design a signal generator to produce chaotic behaviour. By replacing the nonlinear function with memristors in parallel, the memristor oscillator exhibits a chaotic attractor. The simulated results demonstrate that the performance is well predicted by the mathematical analysis and supports the viability of the design

Impact of wind farm wake steering control on blade root load

Yaw misalignment is known to affect blade root loads on wind turbines. Most of previous studies concentrate on yaw misalignment in the context of wake steering control, aiming at increasing the total output power of the wind farm. There, wake steering is compared with greedy control, in which yaw misalignment is considered to be 0. In reality, yaw misalignment also occurs in greedy control due to changes in wind direction arising from varying inflow conditions (e.g. turbulence). This paper aims at comparing these two sources of yaw misalignment-naturally changing wind direction versus active yaw in wake steering-in terms of blade root loads. To this end, SCADA data from a real wind farm is used to get yaw misalignment statistics in actual greedy control conditions. FAST.Farm is used to simulate three wind turbines arranged in series, to study maximum and damage-equivalent loads corresponding to in-plane and out-of-plane bending moments on the blades. The results show that compared with actual greedy control, wake steering control reduces the maximum load from the upstream wind turbine, but increases it from other wind turbines. Concerning the damage-equivalent loads from all wind turbines, the blade's in-plane moment is reduced, but the blade's out-of-plane moment is increased.Impact of wind farm wake steering control on blade root loadacceptedVersio

A Novel Chaotic Neural Network Using Memristive Synapse with Applications in Associative Memory

Chaotic Neural Network, also denoted by the acronym CNN, has rich dynamical behaviors that can be harnessed in promising engineering applications. However, due to its complex synapse learning rules and network structure, it is difficult to update its synaptic weights quickly and implement its large scale physical circuit. This paper addresses an implementation scheme of a novel CNN with memristive neural synapses that may provide a feasible solution for further development of CNN. Memristor, widely known as the fourth fundamental circuit element, was theoretically predicted by Chua in 1971 and has been developed in 2008 by the researchers in Hewlett-Packard Laboratory. Memristor based hybrid nanoscale CMOS technology is expected to revolutionize the digital and neuromorphic computation. The proposed memristive CNN has four significant features: (1) nanoscale memristors can simplify the synaptic circuit greatly and enable the synaptic weights update easily; (2) it can separate stored patterns from superimposed input; (3) it can deal with one-to-many associative memory; (4) it can deal with many-to-many associative memory. Simulation results are provided to illustrate the effectiveness of the proposed scheme

Approximation Order for Multivariate Durrmeyer Operators with Jacobi Weights

Using the equivalence relation between K-functional and modulus of smoothness, we establish a strong direct theorem and an inverse theorem of weak type for multivariate Bernstein-Durrmeyer operators with Jacobi weights on a simplex in this paper. We also obtain a characterization for multivariate Bernstein-Durrmeyer operators with Jacobi weights on a simplex. The obtained results not only generalize the corresponding ones for Bernstein-Durrmeyer operators, but also give approximation order of Bernstein-Durrmeyer operators