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Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements. peerReviewed

Exciton transport can be enhanced in the strong coupling regime where excitons hybridise with confined light modes to form polaritons. Because polaritons have group velocity, their propagation should be ballistic and long-ranged. However, experiments indicate that organic polaritons propagate in a diffusive manner and more slowly than their group velocity. Here, we resolve this controversy by means of molecular dynamics simulations of Rhodamine molecules in a Fabry-P\'{e}rot cavity. Our results suggest that polariton propagation is limited by the cavity lifetime and appears diffusive due to reversible population transfers between polaritonic states that propagate ballistically at their group velocity, and dark states that are stationary. Furthermore, because long-lived dark states transiently trap the excitation, propagation is observed on timescales beyond the intrinsic polariton lifetime. These insights not only help to better understand and interpret experimental observations, but also pave the way towards rational design of molecule-cavity systems for coherent exciton transport.

Sounds emitted by mechanisms and organisms contain information that can be used to diagnose the current state of an object and make predictions. There are known examples of the use of sound for diagnostics of pipelines, composite materials, industrial equipment. In most cases, devices with one sensor and limited functionality are used for this purpose, requiring a specialist to be in close proximity to the object under analysis. The system includes a set of digital microelectromechanical (MEMS) microphones, information from which is transmitted via Bluetooth to the mobile device. The system in a round-the-clock mode quickly registers changes in the spectrum of the sound signaland indicates possible malfunctions, damage to equipment and materials, etc. This allows preventing irreversible consequences. In this system, it is expedient to use digital MEMS microphones due to their low power consumption and low sensitivity to environmental influences, which is an important factor when deploying a remote monitoring system of industrial equipment., Звуки, издаваемые механизмами и организмами, содержат информацию, которую можно использовать для диагностики текущего состояния объекта и прогноза на будущее. Известны примеры использования звука для диагностики трубопроводов, композитных материалов, промышленного оборудования. В большинстве случаев для этой цели применяются устройства с одним датчиком и ограниченным функционалом, требующие нахождения специалиста в непосредственной близости к исследуемому объекту. Предлагается система для дистанционного мониторинга, включающая в себя набор датчиков-микрофонов, информация с которых передается посредством Bluetooth на мобильное устройство. Система в круглосуточном режиме оперативно регистрирует изменения в спектре звукового сигнала, свидетельствующие о возможных неисправностях, повреждении оборудования и материалов и т. д., что позволяет предупредить необратимые последствия. В данной системе целесообразно применять цифровые МЭМС-микрофоны вследствие их низкого энергопотребления и низкой чувствительности к воздействию окружающей среды, что является важным фактором при развертывании системы дистанционного мониторинга промышленного оборудования.

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here we present a general optimization procedure for finding most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated aptamer LC-18t was developed. A three-dimensional shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The truncated aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes. peerReviewed

This deliverable reports on the present state of the BioExcel-2 core application roadmaps, how user and infrastructure needs have been prioritized, the specific tasks this corresponds to in the codes, and what the long-term directions of the codes are – even beyond the present BioExcel funding period. As part of BioExcel2, the software roadmaps have been updated to balance development driven by user requests for features as well as strategic efforts targeting EuroHPC and preparing for next-generation processor and accelerator hardware. The GROMACS development will focus on a number of key user-requested features, in particular adding multiple time stepping, driving simulations with external data, facilitating generation of input data, and better free energy tools. The development of performance optimization for additional new platforms will also continue together with efforts targeting significantly improved scaling by using ensemble parallelism, as well as co-design projects to port the code to new accelerator platforms. The development of the PMX package will follow two main directions. Firstly, the core code will be updated with the changes necessary for the successful future usability of the software. In particular, with the end of Python2 lifetime, pmx will be fully rewritten in Python3. The continuous support of the main pmx functionalities will be ensured. The second major development direction comprises the incorporation of features frequently requested by users, the addition of new mutation libraries and creation of workflows for free energy calculation setup and analysis. HADDOCK’s development focuses on the continuous improvement of the web server, which functions as the main user’s interface, the implementation of relevant features and the design of a new modular version, HADDOCK3. The web server is being co-developed alongside the local HADDOCK version, so that new features (coarse-grained and shape docking, etc.) are readily available in an intuitive and responsive user-friendly interface. A major rework of the current code is in place, for what will become HADDOCK3, with this modular design we aim to provide flexibility for workflow creation and a straightforward framework to integrate new tools. This new modular architecture will also enable more efficient execution on HPC resources. To provide users with access to chemical reactivity in biomolecular simulations, we will develop an interface between GROMACS and CP2K, a highly parallelized density functional theory (DFT) computer program. With the new interface, users can perform multi-scale simulations, in which one part of the system is modelled with DFT, while the remainder is described with a molecular mechanics force field (i.e. QM/MM). Our developments focus on providing the community with an accurate, scalable and user-friendly QM/MM solution. Compared to the previous BioExcel software roadmap, which focused on CPMD for DFT functionality in QM/MM simulations, this updated roadmap reflects the project’s transition to CP2K, which has more wide-spread availability and uptake in the community.

We report the generation of entangled photon pairs at 2090 nm, as a basis for free-space quantum communication in an atmospheric window with low solar background. The source is based on spontaneous parametric down-conversion in periodically poled lithium niobate crystal delivering high coincidence-to-accidental ratio. We demonstrate the two-photon Hong-Ou-Mandel quantum interference and polarization entanglement.

High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and inter-pigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here we report a first principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding QM/MM with the effective fragment potentials (EFP) we were able to compute the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism (CD) spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild type and mutated photosynthetic pigment-protein complexes. peerReviewed

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. Here we briefly outline the challenges associated with such computations and review the progress made in this field. peerReviewed

Quantum-enhanced optical systems operating within the 2- to 2.5-μm spectral region have the potential to revolutionize emerging applications in communications, sensing, and metrology. However, to date, sources of entangled photons have been realized mainly in the near-infrared 700- to 1550-nm spectral window. Here, using custom-designed lithium niobate crystals for spontaneous parametric down-conversion and tailored superconducting nanowire single-photon detectors, we demonstrate two-photon interference and polarization-entangled photon pairs at 2090 nm. These results open the 2- to 2.5-μm mid-infrared window for the development of optical quantum technologies such as quantum key distribution in next-generation mid-infrared fiber communication systems and future Earth-to-satellite communications. Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

Atomic force microscopy (AFM) is widely used to study various biologicalobjects, among others also mammalian cells in physiologically adequate conditions. Force-distance curves provide information about mechanical characteristics of the cell, such as contact stiffness, deformation, Young's modulus etc. Such properties have been linked to various states of disease. AFM studies of the morphology and mechanical properties of native cells can be used in biomedical applications, such as determining the physiological and pathological states of cells. In this work, AFM was applied to examine the mechanical properties of the human umbilical vein endothelial cells (HUVEC) and their dependence on different measurement settings. The influence of the loading rate, maximum load and indenter geometry on the measurement of mechanical properties of such cells has been studied. By applying a linear fitting to a Force-Distance-Curves obtained during nanoindentation experiments the stiffness and the Young’s modulus were calculated. Relation of the mechanical properties of the cells and the experiment condition was demonstrated. Obtained results can be used in a further studies to compare viscoelastic properties of the approach and the retracting curve.

In this work, we show a proof-of-principle benchtop single-photon light detection\ud and ranging (LIDAR) depth imager at 2.3μm, utilizing superconducting nanowire single-photon detectors (SNSPDs). We fabricate and fiber-couple SNSPDs to exhibit enhanced photon counting performance in the mid-infrared. We present characterization results using an optical parametric oscillator source and deploy these detectors in a scanning LIDAR setup at 2.3μm wavelength. This demonstrates the viability of these detectors for future free-space photon counting applications in the mid-infrared where atmospheric absorption and background solar flux are low.

Quantum-enhanced optical systems operating within the 2- to 2.5-$\mu$m spectral region have the potential to revolutionize emerging applications in communications, sensing, and metrology. However, to date, sources of entangled photons have been realized mainly in the near-infrared 700- to 1550-nm spectral window. Here, using custom-designed lithium niobate crystals for spontaneous parametric down-conversion and tailored superconducting nanowire single-photon detectors, we demonstrate two-photon interference and polarization-entangled photon pairs at 2090 nm. These results open the 2- to 2.5-$\mu$m mid-infrared window for the development of optical quantum technologies such as quantum key distribution in next-generation mid-infrared fiber communication systems and future Earth-to-satellite communications.

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra. peerReviewed