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Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the $\lambda$-dynamics approach by Brooks and co-workers was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the $\lambda$-coordinates, not only reduces the complexity associated with parameterizing the intra-molecular interactions between the sites, but is also easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.

In this paper, we consider both energy efficiency and security issues in a wireless power transfer (WPT) enabled relay system. In the considered system, the multiple-antenna decode-and-forward relay node (RN) has both information decoding and wireless power recycling capabilities, and thus can be empowered by WPT and assist the transmission from the multiple-antenna base station (BS) to the mobile terminals (MTs). In addition, we consider that there is an eavesdropper between the BS and the RNs, which tries to overhear the information sent to the MTs. We formulate a joint optimization problem with the objective to optimize energy efficiency of the presented system by considering WPT time allocation, power allocation, and secrecy data rate. In particular, we propose to select RNs based on different assigned priorities so that the physical layer security of information transmission can be guaranteed. Moreover, we take into consideration of the cases that the RNs adopt the half- and full-duplex protocols, and study the corresponding system performance analytically. The proposed schemes are evaluated by extensive simulations and it is demonstrated that the proposed resource allocation schemes can obtain energy efficiency maximization, and have superior performance over other schemes.

AbstractThis article reports on the inclusive production cross section of several quarkonium states, $$\textrm{J}/\psi $$ J / ψ , $$\psi \mathrm{(2S)}$$ ψ ( 2 S ) , $$\Upsilon \mathrm (1S)$$ Υ ( 1 S ) , $$\Upsilon \mathrm{(2S)}$$ Υ ( 2 S ) , and $$\Upsilon \mathrm{(3S)}$$ Υ ( 3 S ) , measured with the ALICE detector at the LHC, in pp collisions at $$\sqrt{s} = 5.02$$ s = 5.02  TeV. The analysis is performed in the dimuon decay channel at forward rapidity ($$2.5< y < 4$$ 2.5 < y < 4 ). The integrated cross sections and transverse-momentum ($$p_{\textrm{T}}$$ p T ) and rapidity ($$y$$ y ) differential cross sections for $$\textrm{J}/\psi $$ J / ψ , $$\psi \mathrm{(2S)}$$ ψ ( 2 S ) , $$\Upsilon \mathrm (1S)$$ Υ ( 1 S ) , and the $$\psi \mathrm{(2S)}$$ ψ ( 2 S ) -to-$$\textrm{J}/\psi $$ J / ψ cross section ratios are presented. The integrated cross sections, assuming unpolarized quarkonia, are: $$\sigma _{\textrm{J}/\psi }$$ σ J / ψ  ($$p_{\textrm{T}} <20$$ p T < 20  GeV/c) = 5.88 ± 0.03 ± 0.34$$ ~\mu $$ μ b, $$\sigma _{\psi \mathrm{(2S)}}$$ σ ψ ( 2 S )  ($$p_{\textrm{T}} <12$$ p T < 12  GeV/c) = 0.87 ± 0.06 ± 0.10$$~\mu $$ μ b, $$\sigma _{\Upsilon \mathrm (1S)}$$ σ Υ ( 1 S )  ($$p_{\textrm{T}} <15$$ p T < 15  GeV/c) = 45.5 ± 3.9 ± 3.5 nb, $$\sigma _{\Upsilon \mathrm{(2S)}}$$ σ Υ ( 2 S )  ($$p_{\textrm{T}} <15$$ p T < 15  GeV/c) = 22.4 ± 3.2 ± 2.7 nb, and $$\sigma _{\Upsilon \mathrm{(3S)}}$$ σ Υ ( 3 S )  ($$p_{\textrm{T}} <15$$ p T < 15  GeV/c) = 4.9 ± 2.2 ± 1.0 nb, where the first (second) uncertainty is the statistical (systematic) one. For the first time, the cross sections of the three $$\Upsilon $$ Υ states, as well as the $$\psi \mathrm{(2S)}$$ ψ ( 2 S ) one as a function of $$p_{\textrm{T}}$$ p T and $$y$$ y , are measured at $$\sqrt{s} = 5.02$$ s = 5.02  TeV at forward rapidity. These measurements also significantly extend the $$\textrm{J}/\psi $$ J / ψ $$p_{\textrm{T}}$$ p T reach and supersede previously published results. A comparison with ALICE measurements in pp collisions at $$\sqrt{s} = 2.76$$ s = 2.76 , 7, 8, and 13 TeV is presented and the energy dependence of quarkonium production cross sections is discussed. Finally, the results are compared with the predictions from several production models.

A lake sediment record from the north-eastern European Russian Arctic was examined using palaeolimnological methods, including subfossil chironomid and diatom analysis. The objective of this study is to disentangle environmental history of the lake and climate variability during the past 2000 years. The sediment profile was divided into two main sections following changes in the lithology, separating the limno-telmatic phase between ~2000 and 1200 cal. yr BP and the lacustrine phase between ~1200 cal. yr BP and the present. Owing to the large proportion of semi-terrestrial chironomids and poor modern analogues, a reliable chironomid-based temperature reconstruction for the limno-telmatic phase was not possible. However, the lacustrine phase showed gradually cooling climate conditions from ~1200 cal. yr BP until ~700 cal. yr BP. The increase in stream chironomids within this sediment section indicates that this period may also have had increased precipitation that caused the adjacent river to overflow, subsequently transporting chironomids to the lacustrine basin. After a short-lived warm phase at ~700 cal. yr BP, the climate again cooled, and a progressive climate warming trend was evident from the most recent sediment samples, where the biological assemblages seem to have experienced an eutrophication-like response to climate warming. The temperature reconstruction showed more similarities with the climate development in the Siberian side of the Urals than with northern Europe. This study provides a characteristic archive of arctic lake ontogeny and a valuable temperature record from a remote climate-sensitive area of northern Russia.