Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches

[Image: see text] Artificial molecular motors (MMs) and switches (MSs), capable of undergoing unidirectional rotation or switching under the appropriate stimuli, are being utilized in multiple complex and chemically diverse environments. Although thorough theoretical work utilizing QM and QM/MM methods have mapped out many of the critical properties of MSs and MMs, as the experimental setups become more complex and ambitious, there is an ever increasing need to study the behavior and dynamics of these molecules as they interact with their environment. To this end, we have parametrized two coarse-grained (CG) models of commonly used MMs and a model for an oxindole-based MS, which can be used to study the ground state behavior of MMs and MSs in large simulations for significantly longer periods of time. We also propose methods to perturb these systems which can allow users to approximate how such systems would respond to MMs rotating or the MSs switching

A facility for investigation of multiple hadrons at cosmic-ray energies

An experimental arrangement for studying multiple hadrons produced in high-energy hadron-nucleus interactions is under construction at the university of Turku. The method of investigation is based on the detection of hadrons arriving simultaneously at sea level over an area of a few square meters. The apparatus consists of a hadron spectrometer with position-sensitive detectors in connection with a small air shower array. The position resolution using streamer tube detectors will be about 10 mm. Energy spectra of hadrons or groups of simultaneous hadrons produced at primary energies below 10 to the 16th power eV can be measured in the energy range 1 to 2000 GeV

Investigation of cosmic rays in very short time scales

A fast databuffer system, where cosmic ray events in the Turku hadron spectrometer, including particle arrival times are recorded with time resolution of 100 ns was constructed. The databuffer can be read continuously by a microprocessor, which preanalyzes the data and transfers it to the main computer. The time span, that can be analyzed in every detail, is a few seconds. The high time resolution enables a study of time correlated groups of high energy particles. In addition the operational characteristics of the spectrometer can be monitored in detail

Spectral analysis of the Forbush decrease of 13 July 1982

The maximum entropy method has been applied in the spectral analysis of high-energy cosmic-ray intensity during the large Forbush event of July 13, 1982. An oscillation with period of about 2 hours and amplitude of 1 to 3% was found to be present during the decrease phase. This oscillation can be related to a similar periodicity in the magnetospheric field. However, the variation was not observed at all neutron monitor stations. In the beginning of the recovery phase, the intensity oscillated with a period of about 10 hours and amplitude of 3%

Observations of cosmic-ray modulations in the fall, 1984

Modulation of cosmic-ray energy spectrum was studied by using the Turku double neutron monitor. The multiplicity region of detected neutrons produced by cosmic ray hadrons in the monitor was divided into seven categories corresponding to mean energies 0.1, 0.3, 1.0, 3.2, 8.6, 21, and 94 GeV of hadrons at sea level. Based on 24-hour frequencies, a statistical analysis showed that modulation of the intensity in all categories occurred during several periods in the fall 1984. The magnitude of the variation was a few per cent

Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes

Plant light-harvesting complex II (LHCII) is the key antenna complex for plant photosynthesis. We present coarse-grained molecular dynamics simulations of monomeric and trimeric LHCII in a realistic thylakoid membrane environment based on the Martini force field. The coarse-grained protein model has been optimized with respect to atomistic reference simulations. Our simulations provide detailed insights in the thylakoid lipid fingerprint of LHCII which compares well with experimental data from membrane protein purification. Comparing the monomer and trimeric LHCII reveals a stabilizing effect of trimerization on the chromophores as well as the protein. Moreover, the average chromophore distance shortens in the trimer leading to stronger excitonic couplings. When changing the native thylakoid environment to a model membrane the protein flexibility remains constant, whereas the chromophore flexibility is reduced. Overall, the presented LHCII model lays the foundation to investigate the μs dynamics of this key antenna protein of plants

Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents:Thermodynamic, Structural, and Extraction Properties

Deep eutectic solvents (DESs) are a more environmentally friendly, cost-effective, and recyclable alternative for ionic liquids. Since the number of possible deep eutectic solvents is very large, there are needs for effective methods to predict the physicochemical nature of possible new deep eutectic solvents that are not met by the currently available models. Here, we have built coarse-grained models for a few well-known and actively studied deep eutectic solvents using the recently published Martini 3 force field. Molecular dynamics simulations demonstrate that our models predict the properties of these particular DESs with an acceptable accuracy, and they are capable of capturing known liquid-liquid extraction processes as well as morphological shape changes of surfactant aggregates. Our coarse-grained approach is novel in the study of DESs, opening new possibilities for rapid screening of new DESs and their properties

Perspective: A stirring role for metabolism in cells

Based on recent findings indicating that metabolism might be governed by a limit on the rate at which cells can dissipate Gibbs energy, in this Perspective, we propose a new mechanism of how metabolic activity could globally regulate biomolecular processes in a cell. Specifically, we postulate that Gibbs energy released in metabolic reactions is used to perform work, allowing enzymes to self‐propel or to break free from supramolecular structures. This catalysis‐induced enzyme movement will result in increased intracellular motion, which in turn can compromise biomolecular functions. Once the increased intracellular motion has a detrimental effect on regulatory mechanisms, this will establish a feedback mechanism on metabolic activity, and result in the observed thermodynamic limit. While this proposed explanation for the identified upper rate limit on cellular Gibbs energy dissipation rate awaits experimental validation, it offers an intriguing perspective of how metabolic activity can globally affect biomolecular functions and will hopefully spark new research

Local C-Reactive Protein Expression in Obliterative Lesions and the Bronchial Wall in Posttransplant Obliterative Bronchiolitis

The local immunoreactivity of C-reactive protein (CRP) was studied in a heterotopic porcine model of posttranplant obliterative bronchiolitis (OB). Bronchial allografts and control autografts were examined serially 2–28 days after subcutaneous transplantation. The autografts stayed patent. In the allografts, proliferation of inflammatory cells (P < .0001) and fibroblasts (P = .02) resulted in occlusion of the bronchial lumens (P < .01). Influx of CD4+ (P < .001) and CD8+ (P < .0001) cells demonstrated allograft immune response. CRP positivity simultaneously increased in the bronchial walls (P < .01), in macrophages, myofibroblasts, and endothelial cells. Local CRP was predictive of features characteristic of OB (R = 0.456–0.879, P < .05−P < .0001). Early obliterative lesions also showed CRP positivity, but not mature, collagen-rich obliterative plugs (P < .05). During OB development, CRP is localized in inflammatory cells, myofibroblasts and endothelial cells probably as a part of the local inflammatory response

Transaortic Transcatheter Aortic Valve Implantation as a second choice over the Transapical access

Background and Aims: In this report, we present our experience with the transaortic transcatheter aortic valve implantation using the SAPIEN valve. The procedural success, 30-day outcome, and survival up to 2years are compared with the transapical access performed in patients in our institution. Material and Methods: Of a total of 282 transcatheter aortic valve implantation patients, 100 consecutive patients had a non-transfemoral approach. The transaortic and transapical access routes were used in 36 and 64 patients, respectively. The transaortic group had a higher mean logistic EuroSCORE (32.6 vs 25.2, p=0.021) and more patients with left ventricular ejection fraction less than 40% (33.3% vs 14.1%, p=0.023). Results: The respective technical success rates for the transaortic and transapical groups were 100% and 95.2% (p=NS). There were significantly more perioperative hemodynamic problems necessitating cardiopulmonary resuscitation or mechanical circulatory support in the transapical group (18.8% vs 2.8%, p=0.023). The transaortic group had a slightly shorter hospital stay (7 vs 8days, p=0.018). The 30-day mortality was 8.6% and 10.9% in the transaortic and transapical group, respectively (p=NS). Combined safety outcome was similar in both groups at 30days. The respective 1-year survival rates for the transaortic and transapical groups were 71.5% and 68.3%, respectively (p=NS). Conclusion: The trans transcatheter aortic valve implantation is a considerable choice to transapical approach. Despite a higher risk patient cohort, the clinical outcome is at least comparable to the transapical transcatheter aortic valve implantation, and it can be utilized as a second choice for patients with prohibitive iliac-femoral anatomy for transfemoral access.Peer reviewe