Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition

Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available

Frequency offset estimation for IFDMA uplink systems

Abstract — This paper proposes two frequency offset estimation algorithms for the uplink of an Interleaved Frequency-Division Multiple-Access (IFDMA) system. One algorithm performs estimation in the frequency domain and the other in the time domain. Both algorithms are based on the maximum likelihood estimation (MLE) principle and use knowledge about pilot symbols. IFDMA utilizes a block-interleaved frequency allocation scheme to exploit the frequency diversity of the channel. In the presence of frequency offsets between users, multiple-access interference (MAI) appears, which has a negative impact on existing frequency offset estimation algorithms. The proposed algorithms are robust, since a special construction of pilot symbols allows to exclude a large amount of MAI in the presence of frequency offsets between users. As a result, the proposed time domain frequency estimation algorithm outperforms the frequency domain algorithm and all other known schemes. I

OFDMA-CDM performance enhancement by combining H-ARQ and interference cancellation

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