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Hybrid coarse-grained and all-atom molecular dynamics simulation studies of binary biological lipid membranes containing chlorosulfolipids

Chlorosulfolipids are the main component of the polar lipid of the flagellar membrane in sea algae and are also known as the major cause of seafood poisoning. Despite the active research on the synthesis of these chlorosulfolipids as potential new drugs, there has been no clear understanding of how they are organized into a stable biological membrane, which is mainly due to their peculiar structure containing hydrophilic sulfate and chloro groups in their tail region. In this study, we have performed hybrid coarse-grained and all-atom molecular dynamics simulations to understand the structural, dynamical, and thermodynamical properties of binary mixture membrane systems consisting of Danicalipin A (DANI), one of the representative chlorosulfolipids, and 1,2-dipalmitoyl-sn-glycero-3-O-4′-(N,N,N-trimethyl)-homoserine (DPTS) lipids. We have observed that at low DANI concentration, DANI is intercalated into one of the leaflets of DPTS bilayer membranes with a y-shaped conformation, consistent with previous experiments. On the other hand, at high DANI concentration, DANI forms a stable monolayer membrane as predicted by our previous simulation study. In the intermediate DANI concentrations, however, DANI molecules tend to reside near the bilayer membrane center to facilitate water penetration through the membrane, affecting the stability of the biological membrane. In addition, there exists a gel-to-liquid crystalline transition in the DANI concentration between 30% and 40%, which was confirmed by both structural and dynamical properties such as the membrane volume, pair distribution function, and diffusion coefficients. We have also investigated the effects of temperature on the phase behavior of the mixture membrane system and found little sensitivity in the range of T = 273–323 K.

Dynamic atrous attention and dual branch context fusion for cross scale Building segmentation in high resolution remote sensing imagery

China’s hydropower megaproject breaks ground

The curious case of how bird wrists evolved

Evaluation of interfacial affinity between surface-modified metal oxide and solvent mixture using molecular dynamics simulations

The industrial application of surface-modified nanoparticles requires controlling their colloidal stability by selecting suitable surface modifiers and solvents. Solvent mixtures can control the interaction between the nanoparticles and solvents, but the detailed mechanism is still unclear. In this study, molecular dynamics simulations were performed for an interface between a decanoic acid-modified Al2O3 and a binary mixture of organic solvents. Cyclohexane and ethanol were selected as a good solvent and a poor solvent for the modifier, respectively, and their volume fraction for preparation was varied. For any volume fraction of ethanol, ethanol was adsorbed onto the Al2O3 surface patches without modifiers. Cyclohexane was preferentially distributed around the modifier. The work of adhesion was calculated as a measure of interfacial affinity using thermodynamic integration. For systems with ethanol, the work of adhesion was significantly larger than for those with cyclohexane, owing to the strong interaction of the Al2O3 surface with the adsorbed ethanol; however, this result, that is, the obtained affinity, is not consistent with the experimental dispersion results of surface-modified nanoparticles. To focus on the interaction between modifiers and surrounding solvents, the work required to strip solvents from the modifier was calculated, excluding the contribution of adsorbed ethanol. The required work decreased after the ethanol fraction surpassed a specific threshold, indicating that the affinity can be related to the distribution of solvent species near the modifier layer. This work provides an evaluation method and insights into the effect of a solvent mixture on the interfacial affinity at the molecular level.

Correction: Inhibition of CDK5 signaling mediated inflammation in macrophages promotes cutaneous wound healing

Unsupervised pretraining in biological neural networks

Abstract Representation learning in neural networks may be implemented with supervised or unsupervised algorithms, distinguished by the availability of instruction. In the sensory cortex, perceptual learning drives neural plasticity1–13, but it is not known whether this is due to supervised or unsupervised learning. Here we recorded populations of up to 90,000 neurons simultaneously from the primary visual cortex (V1) and higher visual areas (HVAs) while mice learned multiple tasks, as well as during unrewarded exposure to the same stimuli. Similar to previous studies, we found that neural changes in task mice were correlated with their behavioural learning. However, the neural changes were mostly replicated in mice with unrewarded exposure, suggesting that the changes were in fact due to unsupervised learning. The neural plasticity was highest in the medial HVAs and obeyed visual, rather than spatial, learning rules. In task mice only, we found a ramping reward-prediction signal in anterior HVAs, potentially involved in supervised learning. Our neural results predict that unsupervised learning may accelerate subsequent task learning, a prediction that we validated with behavioural experiments.

Structure and dynamics of ionic liquids under shear flow

We investigate the intrinsic behavior of ionic liquids under shear flow using a coarse-grained model of [C4mim]+ [PF6]− as a prototypical example. The importance of long-ranged electrostatics is assessed as a function of shear rate by comparing Ewald and reaction field treatments. An appropriate comparison is achieved through the implementation of the proper Lees–Edwards boundary conditions within the ESPResSo++ simulation software. Our results demonstrate that, while structural properties are relatively insensitive to the electrostatic treatment, the more accurate treatment via the Ewald approach is essential for studies of dynamics, in particular, at lower shear rates. Furthermore, we identify a critical shear rate beyond which structural and dynamical properties begin to deviate from equilibrium behavior, while remaining largely unchanged below this threshold. Finally, we demonstrate that the dynamic heterogeneity of the liquid decreases as a function of increasing shear rate, which can be primarily explained by the faster dynamics induced by the shear flow. These results hold relevance for investigations of process-dependent properties of ionic-liquid-based materials.

Slowing down in PNP: relationship of joint velocities in an arm-movement test and the fast TUG test

Abstract Polyneuropathy (PNP) is a prevalent neurological disorder that affects both upper and lower limbs leading to a decline in motor and sensory nerve function and consequently, to movement impairments. In our earlier work, we were able to demonstrate that PNP patients’ slower gait speed as compared to healthy subjects goes along with a relative speed reduction in all major joints of the body during gait, including the arms. It is not known yet, whether this speed reduction is confined to gait or whether it is a general phenomenon of cyclic movements in PNP, which may also show up in isolated goal directed arm movements. We aim here to assess joint speed traces across the body in PNP patients during gait and evaluate the relationship to joint velocities in a different task, i.e. goal directed repetitive arm movements. We compared performances of 20 PNP patients and 20 matched healthy individuals (CG) during (i) the walking sequence of the fast executed TUG test, and (ii) a fast repetitive goal-directed arm-movement test. We were able to reproduce the reduction in joint velocities across all relevant joints during walking. Moreover this reduction of joint velocities was almost evenly distributed across the velocity traces as a function of time. In the goal-directed arm-movement test, PNP patients showed again significantly lower joint velocities across all joints involved (upper body), compared to the CG, with mean and maximum velocities both significantly reduced. The mean velocities of arm-movement test and the degree of slowing observed in the arm-movement task was strongly correlated with TUG performance. Specifically, slower arm movements were associated with longer TUG times (ρ = -0.76, p < 0.001) and reduced gait speed (ρ = 0.79, p < 0.001). Arm movement slowing significantly correlated with clinical scales, including the Falls Efficacy Scale-International (FES-I, ρ = -0.55, p = 0.012) and the Performance-Oriented Mobility Assessment (POMA, ρ = 0.69, p < 0.001). We conclude that the evenly distributed reduction of joint speed as a function of time in PNP is not confined to gait, but also seems to appear in other repetitive motor tasks, here goal-directed arm movements. We assume that joint speed reduction is a general impairment in movement planning and execution of PNP patients. We speculate that this slowing is a consequence of less reliable/ less accurate sensory feedback in the sensorimotor control loop for movement execution. As a clinical application, this finding might help to quantify the amount of the impairment of the sensorimotor control loop in PNP when gait testing is not feasible. Moreover, it might lead to better targeted training strategies to enhance motor performance in PNP. Trial registration: German Clinical Trials Register (DRKS), Identifier: DRKS00016999.

Conjugate-dual clusters

Discovery of clusters with high symmetrical geometry, such as C60 fullerene, always attracts lots of interest because of their diverse nature. However, most of such interesting clusters were sporadically discovered; is there any systematic method to explore all possible high symmetrical clusters? Herein, we propose an idea to systematically construct high symmetrical structures based on a novel conjugate-dual (co-dual) concept. A co-dual structure would be constructed by conjugately combining one high symmetrical polyhedron and its corresponding dual. In such co-dual structures, the symmetry of the original polyhedron could be kept or even promoted in some special cases. This provides a way to explore high symmetrical polyhedra and leads to a new cluster family, co-dual clusters. In this paper, we have systematically studied the spherical co-dual clusters with one- or two-element shells and found a series of stable cage-like and core–shell clusters. The co-dual structures would be a new treasure box for hunting novel clusters.

The epiMelanoma test enables plasma-based detection of melanoma and prediction of immunotherapy response

Spherical to Cartesian coordinates transformation for solid harmonics revisited: Construction of the Hartree potential

Spherical harmonic Gaussian-type orbitals and Slater functions can be expressed using spherical coordinates or linear combinations of the appropriate Cartesian functions. General expressions for the transformation coefficients between the two representations are provided. Values for the transformation coefficients are tabulated up to the quantum number ℓ = 10. The formula is applied to construct the Hartree potential by an arbitrary-order multipole expansion.

Mirabegron nighttime versus daytime dosing for women with overactive bladder syndrome: a randomized controlled trial

Singlet NMR in a case of high molecular symmetry

Spin-1/2 pairs support nuclear singlet and triplet states. The mean population difference between the singlet and triplet manifolds is termed singlet order. Under suitable circumstances, nuclear singlet order is highly resistant to several relaxation mechanisms, displaying a decay time constant TS, which may greatly exceed the time constant T1 for the equilibration of nuclear magnetization. We explore the nuclear singlet relaxation of an isotopolog of squarate in a high-pH aqueous solution. The 1,3–13C2-isotopolog of squarate exists as a minority species of 1–13C2-squarate. This isotopolog has a high degree of molecular symmetry. 18O-enrichment is used to generate secondary isotope shifts of the 13C resonances, providing access to 13C2 double-quantum coherence and 13C2 singlet order. The 13C signals from the 1,2–13C2 and 1,3–13C2 species are selected using geometric double-quantum filtration, and the double-quantum coherence is converted to singlet order and back again using customized double-quantum-to-singlet (DQ2S) and singlet-to-double-quantum (S2DQ) pulse sequences. We report 13C2 singlet lifetime measurements for 1,3–13C2-squarate in a high-pH aqueous solution, in a high magnetic field.

Halomonas sp for sustainable agriculture a potential halo bio fertilizer for tomato plants with biocontrol activity against Fusarium wilt under saline environments

Abstract Halophilic bacteria are remarkable microorganisms that excel in hypersaline environments. Their significant potential in various fields, such as industry and agriculture, positions them as vital players in advancing our technological and ecological efforts. In this study, three bacterial strains (QSLA1, QSLA2, and QSLA3) were successfully isolated from solar saltern ponds, attached to Qarun Lake, Fayoum governorate, Egypt, using nutrient agar (NA) culture medium derived from pond water. Morphological and physiological characterization revealed that these isolates are rod-shaped, gram-negative, catalase-positive, and motile. All isolates were identified as not spore-forming bacteria. The halo tolerance assay demonstrated that QSLA1 and QSLA2 are extremely halophilic, whereas QSLA3 is classified as moderately halophilic. Through 16S rRNA sequence analysis, it was determined that QSLA1 shares 91.26% similarity with Halomonas sp. RS-17, while QSLA2 exhibits 96.6% similarity with Halomonas sp. strain LR2-3. QSLA3 shows even greater similarity at 97.33% to Halomonas sp. GQ30. All isolates are capable of producing indole-3-acetic acid (IAA), but only QSLA2 has the ability to fix atmospheric nitrogen and solubilize insoluble phosphate. Additionally, QSLA1 demonstrates antifungal activity against Fusarium oxysporium f.sp. lycopersici in vitro under saline environment. Given these promising traits, we explored the potential of QSLA1 as a bio-control agent under greenhouse conditions at 1.5% salinity. These findings suggest that these bacterial strains could be used to develop sustainable agricultural practices, enhancing crop yields and reducing the reliance on chemical fertilizers and pesticides. Future applications of these strains could provide a valuable solution for improving agricultural productivity in saline environments.

How changes in behaviour can save lives in disasters

Valence photoelectron spectra of thiouracils in the gas phase

We present a combined experimental and theoretical study of the vibrationally resolved valence photoelectron spectra of the complete series of thiouracils (2-thiouracil, 4-thiouracil, and 2,4-dithiouracil) for binding energies between 8 and 17 eV. The theoretical spectra were calculated using equation-of-motion coupled cluster theory for ionization potential combined with the time-independent double-harmonic adiabatic Hessian approach. For all three thiouracils, the first ionization potential is found between 8.4 and 8.7 eV, which is 1 eV lower than for the canonical nucleobase uracil. Ionization bands up to 12 eV show strong vibrational progressions and are well reproduced by the calculations. These bands are attributed to the ionization of (primarily) sulfur- and oxygen-localized valence molecular orbitals. For higher binding energies, the calculations indicate that nonadiabatic couplings are important for the interpretation of the photoelectron spectra.

The relationship between thermophysiology, endocrinology and behaviour in female giant pandas

Kupffer cell programming by maternal obesity triggers fatty liver disease

Performance of the bond capacity model for charge polarization in classical molecular dynamics

This study investigates the performance of force field models employing only atomic charges to model the electrostatic interactions and only charge-flow to model the electric polarization. The atomic charges and charge-flow parameters are calculated directly by ab initio methods. The performance for liquid-state properties of models that include 1-bond, 2-bond, and 3-bond charge-flow is probed for chloroform and acetonitrile through measurements of dielectric constants, dipole moments, and infrared spectra. The results indicate that models allowing charge-flow only between directly bonded atom pairs (1-bond) lead to significant deviations compared to models incorporating 2- and 3-bond contributions, suggesting that restricting charge-flow solely between directly bonded atom pairs omits important physical contributions. In addition, modeling polarizability via charge-flow inherently leads to an anisotropy description of the molecular polarizability tensor, with the level of anisotropy constituting a major component in the electrostatic response. The results also suggest that modeling the molecular polarizability by only charge-flow tends to overestimate the electric polarization and, thus, indicate that combinations of rank-0 and rank-1 polarizability are required for an accurate modeling of the electric response.