Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification

*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques. Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture identification. 
*Results:* We first formulate the problem of PMF protein mixture identification as an optimization problem. Then, we show that the use of some simple heuristics enables us to find good solutions. As a result, we obtain much better identification results than previous methods. Moreover, the result on real MS data can be comparable with that of the peptide sequencing method. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF method in protein mixtures. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures

Markovian arrivals in stochastic modelling: a survey and some new results

This paper aims to provide a comprehensive review on Markovian arrival processes (MAPs), which constitute a rich class of point processes used extensively in stochastic modelling. Our starting point is the versatile process introduced by Neuts (1979) which, under some simplified notation, was coined as the batch Markovian arrival process (BMAP). On the one hand, a general point process can be approximated by appropriate MAPs and, on the other hand, the MAPs provide a versatile, yet tractable option for modelling a bursty flow by preserving the Markovian formalism. While a number of well-known arrival processes are subsumed under a BMAP as special cases, the literature also shows generalizations to model arrival streams with marks, nonhomogeneous settings or even spatial arrivals. We survey on the main aspects of the BMAP, discuss on some of its variants and generalizations, and give a few new results in the context of a recent state-dependent extension.Peer Reviewe

Radiative thermal switch via metamaterials made of vanadium dioxide-coated nanoparticles

In this work, a thermal switch is proposed based on the phase-change material vanadium dioxide (VO2) within the framework of near-field radiative heat transfer (NFRHT). The radiative thermal switch consists of two metamaterials filled with core-shell nanoparticles, with the shell made of VO2. Compared to traditional VO2 slabs, the proposed switch exhibits a more than 2-times increase in the switching ratio, reaching as high as 90.29% with a 100 nm vacuum gap. The improved switching effect is attributed to the capability of the VO2 shell to couple with the core, greatly enhancing heat transfer with the insulating VO2, while blocking the motivation of the core in the metallic state of VO2. As a result, this efficiently enlarges the difference in photonic characteristics between the insulating and metallic states of the structure, thereby improving the ability to rectify the NFRHT. The proposed switch opens pathways for active control of NFRHT and holds practical significance for developing thermal photon-based logic circuits

Reconstruction of relativistic modified Newtonian dynamics for various cosmological scenarios

In this paper, we present several explicit reconstructions for a novel relativistic theory of modified Newtonian dynamics (RMOND) derived from the background of Friedmann-Lema$\hat{\text{\i}}$tre-Robertson-Walker cosmological evolution. It is shown that the Einstein-Hilbert Lagrangian with a positive cosmological constant is the only Lagrangian capable of accurately replicating the exact expansion history of the $\Lambda$ cold dark matter ($\Lambda$CDM) universe filled solely with dust-like matter and the only way to achieve this expansion history for the RMOND theory is to introduce additional degrees of freedom to the matter sectors. Besides, we find that the $\Lambda$CDM-era also can be replicated without any real matter field within the framework of the RMOND theory and the cosmic evolution exhibited by both the power-law and de-Sitter solutions also can be obtained

[1-(4-Chloro­phen­yl)-5-hy­droxy-3-phenyl-1H-pyrazol-4-yl](thio­phen-2-yl)methanone

In the title compound, C20H13ClN2O2S, the chloro­phenyl, phenyl and thienoyl rings are oriented at dihedral angles 17.84 (7), 53.13 (8) and 34.03 (8)°, respectively, to the central pyrazole ring. An intra­molecular O—H⋯O hydrogen bond occurs. In the crystal, pairs of bifurcated O—H⋯O hydrogen bonds link mol­ecules into inversion dimers with R 2 2(12) graph-set motifs

Multiple magnetoplasmon polaritons of magneto-optical graphene in near-field radiative heat transfer

Graphene, as a two-dimensional magneto-optical material, supports magnetoplasmon polaritons (MPP) when exposed to an applied magnetic field. Recently, MPP of a single-layer graphene has shown an excellent capability in the modulation of near-field radiative heat transfer (NFRHT). In this study, we present a comprehensive theoretical analysis of NFRHT between two multilayered graphene structures, with a particular focus on the multiple MPP effect. We reveal the physical mechanism and evolution law of the multiple MPP, and we demonstrate that the multiple MPP allow one to mediate, enhance, and tune the NFRHT by appropriately engineering the properties of graphene, the number of graphene sheets, the intensity of magnetic fields, as well as the geometric structure of systems. We show that the multiple MPP have a quite significant distinction relative to the single MPP or multiple surface plasmon polaritons (SPPs) in terms of modulating and manipulating NFRHT

Performance improvement of three-body radiative diode driven by graphene surface plasmon polaritons

As an analogue to electrical diode, a radiative thermal diode allows radiation to transfer more efficiently in one direction than in the opposite direction by operating in a contactless mode. In this study, we demonstrated that, within the framework of three-body photon thermal tunneling, the rectification performance of three-body radiative diode can be greatly improved by bringing graphene into the system. The system is composed of three parallel slabs, with the hot and cold terminals of the diode coated with graphene films, and the intermediate body made of vanadium dioxide (VO2). The rectification factor of the proposed radiative thermal diode reaches 300 % with a 350 nm separation distance between the hot and cold terminals of the diode. With the help of graphene, the rectification performance of the radiative thermal diode can be improved by over 11 times. By analyzing the spectral heat flux and energy transmission coefficients, it was found that the improved performance is primarily attributed to the surface plasmon polaritons (SPPs) of graphene. They excite the modes of insulating VO2 in the forward-biased scenario by forming strongly coupled modes between graphene and VO2, and thus dramatically enhance the heat flux. While, for the reverse-biased scenario, the VO2 is at its metallic state and thus graphene SPPs cannot work by three-body photon thermal tunneling. Furthermore, the improvement was also investigated for different chemical potentials of graphene, and geometric parameters of the three-body system. Our findings demonstrate the feasibility of using thermal-photon-based logical circuits, creating radiation-based communication technology, and implementing thermal management approaches at the nanoscale