Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

We describe AlphaFold, the protein structure prediction system that was entered by the group A7D in CASP13 Submissions were made by three free-modelling methods which combine the predictions of three neural networks. All three systems were guided by predictions of distances between pairs of residues produced by a neural network. Two systems assembled fragments produced by a generative neural network, one using scores from a network trained to regress GDT_TS. The third system shows that simple gradient descent on a properly constructed potential is able to perform on-par with more expensive traditional search techniques and without requiring domain segmentation. In the CASP13 free-modelling assessors' ranking by summed z-scores, this system scored highest with 68.3 vs 48.2 for the next closest group. (An average GDT_TS of 61.4.) The system produced high-accuracy structures (with GDT_TS scores of 70 or higher) for 11 out of 43 free-modelling domains. Despite not explicitly using template information, the results in the template category were comparable to the best performing template-based methods

Genotyping a second growth coast redwood forest : a high throughput methodology

The idea that excitonic (electronic) coherences are of fundamental importance to natural photosynthesis gained popularity when slowly dephasing quantum beats (QBs) were observed in the two-dimensional electronic spectra of the Fenna–Matthews–Olson (FMO) complex at 77 K. These were assigned to superpositions of excitonic states, a controversial interpretation, as the strong chromophore–environment interactions in the complex suggest fast dephasing. Although it has been pointed out that vibrational motion produces similar spectral signatures, a concrete assignment of these oscillatory signals to distinct physical processes is still lacking. Here we revisit the coherence dynamics of the FMO complex using polarization-controlled two-dimensional electronic spectroscopy, supported by theoretical modelling. We show that the long-lived QBs are exclusively vibrational in origin, whereas the dephasing of the electronic coherences is completed within 240 fs even at 77 K. We further find that specific vibrational coherences are produced via vibronically coupled excited states. The presence of such states suggests that vibronic coupling is relevant for photosynthetic energy transfer

Data processing correction of the irising effect of a fast-gating intensified charge-coupled device on laser-pulse-excited luminescence spectra

Intensified charge-coupled devices (ICCDs) comprise the advantages of both fast gating detectors and spectrally broad CCDs into one device that enables temporally and spectrally resolved measurements with a few nanosecond resolution. Gating of the measured signal occurs in the image intensifier tube, where a high voltage is applied between the detector photocathode and a microchannel plate electron multiplier. An issue arises in time-resolved luminescence spectroscopy when signal onset characterization is required. In this case, the transient gate closing process that causes the detected signal always arises in the middle of the ICCD chip regardless of the spectral detection window—the so-called irising effect. We demonstrate that in case when the detection gate width is comparable to the opening/closing time and the gate is pretriggered with respect to the signal onset, the irising effect causes the obtained data to be strongly distorted. At the same time, we propose a software procedure that leads to the spectral correction of the irising effect and demonstrate its validity on the distorted data

Femtosecond luminescence spectroscopy of core states in silicon nanocrystals

We present a study of ultrafast carrier transfer from highly luminescent states inside the core of silicon nanocrystal (due to quasidirect transitions) to states on the nanocrystal-matrix interface. This transfer leads to a sub-picosecond luminescence decay, which is followed by a slower decay component induced by carrier relaxation to lower interface states. We investigate the luminescence dynamics for two different surface passivation types and we propose a general model describing spectral dependence of ultrafast carrier dynamics. Our results stress the crucial role of the energy distribution of the interface states on surface-related quenching of quasidirect luminescence in silicon nanocrystals. We discuss how to avoid this quenching in order to bring the attractive properties of the quasidirect recombination closer to exploitation

Brightly luminescent organically capped silicon nanocrystals fabricated at room temperature and atmospheric pressure

Silicon nanocrystals are an extensively studied light-emitting material due to their inherent biocompatibility and compatibility with silicon-based technology. Although they might seem to fall behind their rival, namely, direct band gap based semiconductor nanocrystals, when it comes to the emission of light, room for improvement still lies in the exploitation of various surface passivations. In this paper, we report on an original way, taking place at room temperature and ambient pressure, to replace the silicon oxide shell of luminescent Si nanocrystals with capping involving organic residues. The modification of surface passivation is evidenced by both Fourier transform infrared spectroscopy and nuclear magnetic resonance measurements. In addition, single-nanocrystal spectroscopy reveals the occurrence of a systematic fine structure in the emission single spectra, which is connected with an intrinsic property of small nanocrystals since a very similar structure has recently been observed in specially passivated semiconductor CdZnSe nanoparticles. The organic capping also dramatically changes optical properties of Si nanocrystals (resulting ensemble photoluminescence quantum efficiency 20%, does not deteriorate, radiative lifetime 10 ns at 550 nm at room temperature). Optically clear colloidal dispersion of these nanocrystals thus exhibits properties fully comparable with direct band gap semiconductor nanoparticles