X-Ray Calc 3: improved software for simulation and inverse problem solving for X-ray reflectivity

This work introduces X-Ray Calc (XRC), an open-source software package designed to simulate X-ray reflectivity (XRR) and address the inverse problem of reconstructing film structures on the basis of measured XRR curves. XRC features a user-friendly graphical interface that facilitates interactive simulation and reconstruction. The software employs a recursive approach based on the Fresnel equations to calculate XRR and incorporates specialized tools for modeling periodic multilayer structures. This article presents the latest version of the X-Ray Calc software (XRC3), with notable improvements. These enhancements encompass an automatic fitting capability for XRR curves utilizing a modified flight particle swarm optimization algorithm. A novel cost function was also developed specifically for fitting XRR curves of periodic structures. Furthermore, the overall user experience has been enhanced by developing a new single-window interface.

Development, validation, and simplification of a scanner-specific CT simulator

BACKGROUND

Simulated computed tomography (CT) images allow for knowledge of the underlying ground truth and for easy variation of imaging conditions, making them ideal for testing and optimization of new applications or algorithms. However, simulating all processes that affect CT images can result in simulations that are demanding in terms of processing time and computer memory. Therefore, it is of interest to determine how much the simulation can be simplified while still achieving realistic results.

PURPOSE

To develop a scanner-specific CT simulation using physics-based simulations for the position-dependent effects and shift-invariant image corruption methods for the detector effects. And to investigate the impact on image realism of introducing simplifications in the simulation process that lead to faster and less memory-demanding simulations.

METHODS

To make the simulator realistic and scanner-specific, the spatial resolution and noise characteristics, and the exposure-to-detector output relationship of a clinical CT system were determined. The simulator includes a finite focal spot size, raytracing of the digital phantom, gantry rotation during projection acquisition, and finite detector element size. Previously published spectral models were used to model the spectrum for the given tube voltage. The integrated energy at each element of the detector was calculated using the Beer-Lambert law. The resulting angular projections were subsequently corrupted by the detector modulation transfer function (MTF), and by addition of noise according to the noise power spectrum (NPS) and signal mean-variance relationship, which were measured for different scanner settings. The simulated sinograms were reconstructed on the clinical CT system and compared to real CT images in terms of CT numbers, noise magnitude using the standard deviation, noise frequency content using the NPS, and spatial resolution using the MTF throughout the field of view (FOV). The CT numbers were validated using a multi-energy CT phantom, the noise magnitude and frequency were validated with a water phantom, and the spatial resolution was validated with a tungsten wire. These metrics were compared at multiple scanner settings, and locations in the FOV. Once validated, the simulation was simplified by reducing the level of subsampling of the focal spot area, rotation and of detector pixel size, and the changes in MTFs were analyzed.

RESULTS

The average relative errors for spatial resolution within and across image slices, noise magnitude, and noise frequency content within and across slices were 3.4%, 3.3%, 4.9%, 3.9%, and 6.2%, respectively. The average absolute difference in CT numbers was 10.2 HU and the maximum was 22.5 HU. The simulation simplification showed that all subsampling can be avoided, except for angular, while the error in frequency at 10% MTF would be maximum 16.3%.

CONCLUSION

The simulation of a scanner-specific CT allows for the generation of realistic CT images by combining physics-based simulations for the position-dependent effects and image-corruption methods for the shift-invariant ones. Together with the available ground truth of the digital phantom, it results in a useful tool to perform quantitative analysis of reconstruction or post-processing algorithms. Some simulation simplifications allow for reduced time and computer power requirements with minimal loss of realism.

Natural and Synthetic Coumarins as Potential Drug Candidates Against SARS-CoV-2/CoViD-19

COVID-19, an airborne disease caused by a betacoronavirus named SARS-- CoV-2, was officially declared a pandemic in early 2020, resulting in more than 770 million confirmed cases and over 6.9 million deaths by September 2023. Although the introduction of vaccines in late 2020 helped reduce the number of deaths, the global effort to fight COVID-19 is far from over. While significant progress has been made in a short period, the fight against SARS-CoV-2/COVID-19 and other potential pandemic threats continues. Like AIDS and hepatitis C epidemics, controlling the spread of COVID-19 will require the development of multiple drugs to weaken the virus's resistance to different drug treatments. Therefore, it is essential to continue developing new drug candidates derived from natural or synthetic small molecules. Coumarins are a promising drug design and development scaffold due to their synthetic versatility and unique physicochemical properties. Numerous examples reported in scientific literature, mainly by in silico prospection, demonstrate their potential contribution to the rapid development of drugs against SARS-CoV-2/COVID-19 and other emergent and reemergent viruses.

Spontaneous Synchronization of Two Bistable Pyridine-Furan Nanosprings Connected by an Oligomeric Bridge

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose long-term conformational dynamics are similar to the dynamics of bistable mechanical systems such as Euler arches and Duffing oscillators. Collective synchrony in bistable dynamics of molecular-sized systems has attracted immense attention as a potential pathway to amplify the output signals of molecular nanodevices. Recently, pyridine-furan oligomers of helical shape that are a few nanometers in size and exhibit bistable dynamics similar to a Duffing oscillator have been identified through molecular dynamics simulations. In this article, we present the case of dynamical synchronization of these bistable systems. We show that two pyridine-furan springs connected by a rigid oligomeric bridge spontaneously synchronize vibrations and stochastic resonance enhances the synchronization effect.

Membrane-Mediated Cooperative Interactions of CD47 and SIRPα

The specific binding of the ubiquitous 'marker of self' protein CD47 to the SIRPα protein anchored in the macrophage plasma membrane results in the inhibition of the engulfment of 'self' cells by macrophages and thus constitutes a key checkpoint of our innate immune system. Consequently, the CD47-SIRPα protein complex has been recognized as a potential therapeutic target in cancer and inflammation. Here, we introduce a lattice-based mesoscale model for the biomimetic system studied recently in fluorescence microscopy experiments where GFP-tagged CD47 proteins on giant plasma membrane vesicles bind to SIRPα proteins immobilized on a surface. Computer simulations of the lattice-based mesoscale model allow us to study the biomimetic system on multiple length scales, ranging from single nanometers to several micrometers and simultaneously keep track of single CD47-SIRPα binding and unbinding events. Our simulations not only reproduce data from the fluorescence microscopy experiments but also are consistent with results of several other experiments, which validates our numerical approach. In addition, our simulations yield quantitative predictions on the magnitude and range of effective, membrane-mediated attraction between CD47-SIRPα complexes. Such detailed information on CD47-SIRPα interactions cannot be obtained currently from experiments alone. Our simulation results thus extend the present understanding of cooperative effects in CD47-SIRPα interactions and may have an influence on the advancement of new cancer treatments.

Clinical value of CT-derived simulations of transcatheter-aortic-valve-implantation in challenging anatomies the PRECISE-TAVI trial

BACKGROUND

Preprocedural computed tomography planning improves procedural safety and efficacy of transcatheter aortic valve implantation (TAVI). However, contemporary imaging modalities do not account for device-host interactions.

AIMS

This study evaluates the value of preprocedural computer simulation with FEops HEARTguideTM on overall device success in patients with challenging anatomies undergoing TAVI with a contemporary self-expanding supra-annular transcatheter heart valve.

METHODS

This prospective multicenter observational study included patients with a challenging anatomy defined as bicuspid aortic valve, small annulus or severely calcified aortic valve. We compared the heart team's transcatheter heart valve (THV) planning decision based on (1) conventional multislice computed tomography (MSCT) and (2) MSCT imaging with FEops HEARTguideTM simulations. Clinical outcomes and THV performance were followed up to 30 days.

RESULTS

A total of 77 patients were included (median age 79.9 years (IQR 74.2-83.8), 42% male). In 35% of the patients, preprocedural planning changed after FEops HEARTguideTM simulations (change in valve size selection [12%] or target implantation height [23%]). A new permanent pacemaker implantation (PPI) was implanted in 13% and >trace paravalvular leakage (PVL) occurred in 28.5%. The contact pressure index (i.e., simulation output indicating the risk of conduction abnormalities) was significantly higher in patients with a new PPI, compared to those without (16.0% [25th-75th percentile 12.0-21.0] vs. 3.5% [25th-75th percentile 0-11.3], p < 0.01) The predicted PVL was 5.7 mL/s (25th-75th percentile 1.3-11.1) in patients with none-trace PVL, 12.7 (25th-75th percentile 5.5-19.1) in mild PVL and 17.7 (25th-75th percentile 3.6-19.4) in moderate PVL (p = 0.04).

CONCLUSION

FEops HEARTguideTM simulations may provide enhanced insights in the risk for PVL or PPI after TAVI with a self-expanding supra-annular THV in complex anatomies.

Partitioning variance in reproductive success, within years and across lifetimes

Variance in reproductive success (s k 2 , with k = number of offspring) plays a large role in determining the rate of genetic drift and the scope within which selection acts. Various frameworks have been proposed to parse factors that contribute to s k 2 , but none has focused on age-specific values of ϕ = s k 2 / k ¯ , which indicate the degree to which reproductive skew is overdispersed (compared to the random Poisson expectation) among individuals of the same age and sex. Instead, within-age effects are generally lumped with residual variance and treated as "noise." Here, an ANOVA sums-of-squares framework is used to partition variance in annual and lifetime reproductive success into between-group and within-group components. For annual reproduction, the between-age effect depends on age-specific fecundity (b x), but relatively few empirical data are available on the within-age effect, which depends on ϕ x. By defining groups by age-at-death rather than age, the same ANOVA framework can be used to partition variance in lifetime reproductive success (LRS) into between-group and within-group components. Analytical methods are used to develop null-model expectations for random contributions to within-group and between-group components. For analysis of LRS, random variation in longevity appears as part of the between-group variance, and effects (if any) of skip breeding and persistent individual differences contribute to the within-group variance. Simulations are used to show that the methods for variance partitioning are asymptotically unbiased. Practical application is illustrated with empirical data for annual reproduction in American black bears and lifetime reproduction in Dutch great tits. Results show that overdispersed within-age variance (1) dominates annual s k 2 in both male and female black bears, (2) is the primary factor that reduces annual effective size to a fraction of the number of adults, and (3) represents most of the opportunity for selection. In contrast, about a quarter of the variance in LRS in great tits can be attributed to random variation in longevity, and most of the rest is due to modest differences in fecundity with age estimated for a single cohort of females. R code is provided that reads generic input files for annual and lifetime reproductive success and allows users to conduct variance partitioning with their own data.

Simulation as a tool to model potential workflow enhancements in radiotherapy treatment pathways - A systematic review

This systematic review aimed to synthesize and summarize the use of simulation of radiotherapy pathways. The objective was to establish the suitability of those simulations in modeling the potential introduction of processes and technologies to speed up radiotherapy pathways. A systematic literature search was carried out using PubMed and Scopus databases to evaluate the use of simulation in radiotherapy pathways. Full journal articles and conference proceedings were considered, and the search was limited to the English language only. To be eligible for inclusion, articles had to model multiple sequential processes in the radiotherapy pathway concurrently to demonstrate the suitability of simulation modeling in typical pathways. Papers solely modeling scheduling, capacity, or queuing strategies were excluded. In total, 151 potential studies were identified and screened to find 18 relevant studies in October 2022. Studies showed that various pathways could be modeled, including the entire pathway from referral to end of treatment or the constituent phases such as pre-treatment, treatment, or other subcomponents. The data required to generate models varied from study to study, but at least 3 months of data were needed. This review demonstrates that modeling and simulation of radiotherapy pathways are feasible and that model output matches real-world systems. Validated models give researchers confidence to modify models with potential workflow enhancements to assess their potential effect on real-world systems. It is recommended that researchers follow best practice guidelines when building models to ensure that they are fit for purpose and to enable decision makers to have confidence in their results.

Impact of Inclination of Girders and Columns on the Effort and Stability of Flat Bar Frames

The article describes a specific method of using innovative transverse systems of flat bar frames as structures forcing elastic shape transformations of nominally flat folded sheets into the forms of ruled shell roof coverings. An innovative method for parametric shaping these forms and arrangement of frames constituting structural systems of sheds with folded thin-walled roof coverings, taking account of the specificity of designing elastically transformed roof sheeting, was proposed. The proposed method for defining the loads of the considered frames supporting lower shelves of the folds of transformed roof sheeting, as loads distributed uniformly along the length of the upper chord of a roof frame girder, is also an innovative approach. The above unconventional premises result in the innovative topic of the research presented in terms of checking the impact of changing the shape of subsequent flat frames (intended for the construction of sheds roofed with the transformed sheeting) on the geometric and mechanical properties of the members of these frames. For the defined loads and the proposed parameterization of the frame forms, an innovative set of conditions was developed to optimize their performance, and then a theoretical analysis of the observed dependencies was carried out. This analysis was performed in an unconventional, novel way using section modules of the cross-sections of all members. The performed computer simulations confirmed the significance of changes in the inclination of girders and columns on the geometric and mechanical properties of the members. The obtained results are the basis and justification for simulations and tests in the scope of further modification of the form, loads, work, and methods of using various configurations of flat frames in constructions.

Molecular Dynamics Simulation of Hydrogels Based on Phosphorylcholine-Containing Copolymers for Soft Contact Lens Applications

The structure and dynamics of copolymers of 2-hydroxyethyl methacrylate (HEMA) with 2-methacryloyloxyethyl phosphorylcholine (MPC) were studied by molecular dynamics simulations. In total, 20 systems were analyzed. They differed in numerical fractions of the MPC in the copolymer chain, equal to 0.26 and 0.74, in the sequence of mers, block and random, and the water content, from 0 to 60% by mass. HEMA side chains proved relatively rigid and stable in all considered configurations. MPC side chains, in contrast, were mobile and flexible. Water substantially influenced their dynamics. The copolymer swelling caused by water resulted in diffusion channels, pronounced in highly hydrated systems. Water in the hydrates existed in two states: those that bond to the polymer chain and the free one; the latter was similar to bulk water but with a lower self-diffusion coefficient. The results proved that molecular dynamics simulations could facilitate the preliminary selection of the polymer materials for specific purposes before their synthesis.

The Action Potential Clamp Technique as a Tool for Risk Stratification of Sinus Bradycardia Due to Loss-of-Function Mutations in HCN4: An In Silico Exploration Based on In Vitro and In Vivo Data

These days, in vitro functional analysis of gene variants is becoming increasingly important for risk stratification of cardiac ion channelopathies. So far, such risk stratification has been applied to SCN5A, KCNQ1, and KCNH2 gene variants associated with Brugada syndrome and long QT syndrome types 1 and 2, respectively, but risk stratification of HCN4 gene variants related to sick sinus syndrome has not yet been performed. HCN4 is the gene responsible for the hyperpolarization-activated 'funny' current If, which is an important modulator of the spontaneous diastolic depolarization underlying the sinus node pacemaker activity. In the present study, we carried out a risk classification assay on those loss-of-function mutations in HCN4 for which in vivo as well as in vitro data have been published. We used the in vitro data to compute the charge carried by If (Qf) during the diastolic depolarization phase of a prerecorded human sinus node action potential waveform and assessed the extent to which this Qf predicts (1) the beating rate of the comprehensive Fabbri-Severi model of a human sinus node cell with mutation-induced changes in If and (2) the heart rate observed in patients carrying the associated mutation in HCN4. The beating rate of the model cell showed a very strong correlation with Qf from the simulated action potential clamp experiments (R2 = 0.95 under vagal tone). The clinically observed minimum or resting heart rates showed a strong correlation with Qf (R2 = 0.73 and R2 = 0.71, respectively). While a translational perspective remains to be seen, we conclude that action potential clamp on transfected cells, without the need for further voltage clamp experiments and data analysis to determine individual biophysical parameters of If, is a promising tool for risk stratification of sinus bradycardia due to loss-of-function mutations in HCN4. In combination with an If blocker, this tool may also prove useful when applied to human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) obtained from mutation carriers and non-carriers.

Location and Concentration of Aromatic-Rich Segments Dictates the Percolating Inter-Molecular Network and Viscoelastic Properties of Ageing Condensates

Maturation of functional liquid-like biomolecular condensates into solid-like aggregates has been linked to the onset of several neurodegenerative disorders. Low-complexity aromatic-rich kinked segments (LARKS) contained in numerous RNA-binding proteins can promote aggregation by forming inter-protein β-sheet fibrils that accumulate over time and ultimately drive the liquid-to-solid transition of the condensates. Here, atomistic molecular dynamics simulations are combined with sequence-dependent coarse-grained models of various resolutions to investigate the role of LARKS abundance and position within the amino acid sequence in the maturation of condensates. Remarkably, proteins with tail-located LARKS display much higher viscosity over time than those in which the LARKS are placed toward the center. Yet, at very long timescales, proteins with a single LARKS-independently of its location-can still relax and form high viscous liquid condensates. However, phase-separated condensates of proteins containing two or more LARKS become kinetically trapped due to the formation of percolated β-sheet networks that display gel-like behavior. Furthermore, as a work case example, they demonstrate how shifting the location of the LARKS-containing low-complexity domain of FUS protein toward its center effectively precludes the accumulation of β-sheet fibrils in FUS-RNA condensates, maintaining functional liquid-like behavior without ageing.

Impacts of Halogen Substitutions on Bisphenol A Compounds Interaction with Human Serum Albumin: Exploring from Spectroscopic Techniques and Computer Simulations

Bisphenol A (BPA) is an endocrine-disrupting compound, and the binding mechanism of BPA with carrier proteins has drawn widespread attention. Halogen substitutions can significantly impact the properties of BPA, resulting in various effects for human health. Here, we selected tetrabromobisphenol A (TBBPA) and tetrachlorobisphenol A (TCBPA) to investigate the interaction between different halogen-substituted BPAs and human serum albumin (HSA). TBBPA/TCBPA spontaneously occupied site I and formed stable binary complexes with HSA. Compared to TCBPA, TBBPA has higher binding affinity to HSA. The effect of different halogen substituents on the negatively charged surface area of BPA was an important reason for the higher binding affinity of TBBPA to HSA compared to TCBPA. Hydrogen bonds and van der Waals forces were crucial in the TCBPA-HSA complex, while the main driving factor for the formation of the TBBPA-HSA complex was hydrophobic interactions. Moreover, the presence of TBBPA/TCBPA changed the secondary structure of HSA. Amino acid residues such as Lys199, Lys195, Phe211, Arg218, His242, Leu481, and Trp214 were found to play crucial roles in the binding process between BPA compounds and HSA. Furthermore, the presence of halogen substituents facilitated the binding of BPA compounds with HSA.

Prediction of Grain Size in a High Cobalt Nickel-Based Superalloy

With the advancement in computational approaches and experimental, simulation, and modeling tools in recent decades, a trial-and-validation method is attracting more attention in the materials community. The development of powder metallurgy Ni-based superalloys is a vivid example that relies on simulation and experiments to produce desired microstructure and properties in a tightly controlled manner. In this research, we show an integrated approach to predicting the grain size of industrial forgings starting from lab-scale cylindrical compression by employing modeling and experimental validation. (a) Cylindrical compression tests to obtain accurate flow stress data and the hot working processing window; (b) double-cone tests of laboratory scale validation; (c) sub-scale forgings for further validation under production conditions; and (d) application and validation on full-scale industrial forgings. The procedure uses modeling and simulation to predict metal flow, strain, strain rate, temperature, and the resulting grain size as a function of thermo-mechanical processing conditions. The models are calibrated with experimental data until the accuracy of the modeling predictions is at an acceptable level, which is defined as the accuracy at which the results can be used to design and evaluate industrial forgings.

Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP

Adaptive capacity can present challenges for modelling as it encompasses multiple ecological and evolutionary processes such as natural selection, genetic drift, gene flow and phenotypic plasticity. Spatially explicit, individual-based models provide an outlet for simulating these complex interacting eco-evolutionary processes. We expanded the existing Cost-Distance Meta-POPulation (CDMetaPOP) framework with inducible plasticity modelled as a habitat selection behaviour, using temperature or habitat quality variables, with a genetically based selection threshold conditioned on past individual experience. To demonstrate expected results in the new module, we simulated hypothetical populations and then evaluated model performance in populations of redband trout (Oncorhynchus mykiss gairdneri) across three watersheds where temperatures induce physiological stress in parts of the stream network. We ran simulations using projected warming stream temperature data under four scenarios for alleles that: (1) confer thermal tolerance, (2) bestow plastic habitat selection, (3) give both thermal tolerance and habitat selection preference and (4) do not provide either thermal tolerance or habitat selection. Inclusion of an adaptive allele decreased declines in population sizes, but this impact was greatly reduced in the relatively cool stream networks. As anticipated with the new module, high-temperature patches remained unoccupied by individuals with the allele operating plastically after exposure to warm temperatures. Using complete habitat avoidance above the stressful temperature threshold, habitat selection reduced the overall population size due to the opportunity cost of avoiding areas with increased, but not guaranteed, mortality. Inclusion of plasticity within CDMetaPOP will provide the potential for genetic or plastic traits and 'rescue' to affect eco-evolutionary dynamics for research questions and conservation applications.

Simulation of Corrosion Phenomena in Automotive Components: A Case Study

Mathematical modelling and software simulation nowadays are very effective tools for both understanding and predicting corrosion processes and the protection of metallic components. COMSOL Multiphysics 5.6 software provides validated mathematical models that can be used, for a given geometry, as a tool to predict and prevent corrosion of components. The corrosion of zinc-coated steel sheets has been studied in this work by comparing results of the simulations with laboratory tests carried out in a salt spray. Results of both the mathematical modelling and empirical tests give the possibility to estimate the stability of the protective zinc layer over time. The examination of the discrepancies between two analytical methods for the investigation of corrosion phenomena leads to possible modifications in the model in order to reach as much as possible coherence with experimental data. As a final result, a computational model of corrosion phenomena in an automotive component has been reached, allowing in the future to partially substitute laboratory tests, usually being highly time consuming and expensive.

Evolutionary potential mitigates extinction risk under climate change in the endangered southwestern willow flycatcher

The complexity of global anthropogenic change makes forecasting species responses and planning effective conservation actions challenging. Additionally, important components of a species' adaptive capacity, such as evolutionary potential, are often not included in quantitative risk assessments due to lack of data. While genomic proxies for evolutionary potential in at-risk species are increasingly available, they have not yet been included in extinction risk assessments at a species-wide scale. In this study, we used an individual-based, spatially explicit, dynamic eco-evolutionary simulation model to evaluate the extinction risk of an endangered desert songbird, the southwestern willow flycatcher (Empidonax traillii extimus), in response to climate change. Using data from long-term demographic and habitat studies in conjunction with genome-wide ecological genomics research, we parameterized simulations that include 418 sites across the breeding range, genomic data from 225 individuals, and climate change forecasts spanning 3 generalized circulation models and 3 emissions scenarios. We evaluated how evolutionary potential, and the lack of it, impacted population trajectories in response to climate change. We then investigated the compounding impact of drought and warming temperatures on extinction risk through the mechanism of increased nest failure. Finally, we evaluated how rapid action to reverse greenhouse gas emissions would influence population responses and species extinction risk. Our results illustrate the value of incorporating evolutionary, demographic, and dispersal processes in a spatially explicit framework to more comprehensively evaluate the extinction risk of threatened and endangered species and conservation actions to promote their recovery.

Emergent structural correlations in dense liquids

The complete quantitative description of the structure of dense and supercooled liquids remains a notoriously difficult problem in statistical physics. Most studies to date focus solely on two-body structural correlations, and only a handful of papers have sought to consider additional three-body correlations. Here, we go beyond the state of the art by extracting many-body static structure factors from molecular dynamics simulations and by deriving accurate approximations up to the six-body structure factor via density functional theory. We find that supercooling manifestly increases four-body correlations, akin to the two- and three-body case. However, at small wave numbers, we observe that the four-point structure of a liquid drastically changes upon supercooling, both qualitatively and quantitatively, which is not the case in two-point structural correlations. This indicates that theories of the structure or dynamics of dense liquids should incorporate many-body correlations beyond the two-particle level to fully capture their intricate behavior.

Plasmid Costs Explain Plasmid Maintenance, Irrespective of the Nature of Compensatory Mutations

Conjugative plasmids often carry virulence and antibiotic-resistant genes. Therefore, understanding the behavior of these extra-chromosomal DNA elements gives insights into their spread. Bacteria frequently replicate slower after plasmids' entry, an observation inconsistent with the plasmids' ubiquity in nature. Several hypotheses explain the maintenance of plasmids among bacterial communities. However, the numerous combinations of bacterial species and strains, plasmids, and environments claim a robust elucidatory mechanism of plasmid maintenance. Previous works have shown that donor cells already adapted to the plasmid may use the plasmid as a 'weapon' to compete with non-adapted plasmid-free cells. Computer simulations corroborated this hypothesis with a wide range of parameters. Here we show that donor cells benefit from harboring conjugative plasmids even if compensatory mutations in transconjugant cells occur in the plasmid, not on chromosomes. The advantage's leading causes are as follows: mutations take time to appear, many plasmids remain costly, and re-transfer of mutated plasmids usually occurs in sites distant to the original donors, implying little competition between these cells. Research in previous decades cautioned against uncritical acceptance of the hypothesis that resistance cost helps to preserve antibiotics' effectiveness. This work gives a new twist to this conclusion by showing that costs help antibiotic-resistant bacteria to compete with plasmid-free cells even if compensatory mutations appear in plasmids.

Human Sinoatrial Node Pacemaker Activity: Role of the Slow Component of the Delayed Rectifier K+ Current, IKs

The pacemaker activity of the sinoatrial node (SAN) has been studied extensively in animal species but is virtually unexplored in humans. Here we assess the role of the slowly activating component of the delayed rectifier K+ current (IKs) in human SAN pacemaker activity and its dependence on heart rate and β-adrenergic stimulation. HEK-293 cells were transiently transfected with wild-type KCNQ1 and KCNE1 cDNA, encoding the α- and β-subunits of the IKs channel, respectively. KCNQ1/KCNE1 currents were recorded both during a traditional voltage clamp and during an action potential (AP) clamp with human SAN-like APs. Forskolin (10 µmol/L) was used to increase the intracellular cAMP level, thus mimicking β-adrenergic stimulation. The experimentally observed effects were evaluated in the Fabbri-Severi computer model of an isolated human SAN cell. Transfected HEK-293 cells displayed large IKs-like outward currents in response to depolarizing voltage clamp steps. Forskolin significantly increased the current density and significantly shifted the half-maximal activation voltage towards more negative potentials. Furthermore, forskolin significantly accelerated activation without affecting the rate of deactivation. During an AP clamp, the KCNQ1/KCNE1 current was substantial during the AP phase, but relatively small during diastolic depolarization. In the presence of forskolin, the KCNQ1/KCNE1 current during both the AP phase and diastolic depolarization increased, resulting in a clearly active KCNQ1/KCNE1 current during diastolic depolarization, particularly at shorter cycle lengths. Computer simulations demonstrated that IKs reduces the intrinsic beating rate through its slowing effect on diastolic depolarization at all levels of autonomic tone and that gain-of-function mutations in KCNQ1 may exert a marked bradycardic effect during vagal tone. In conclusion, IKs is active during human SAN pacemaker activity and has a strong dependence on heart rate and cAMP level, with a prominent role at all levels of autonomic tone.

Sulfate and acid-base balance

It has been acknowledged for years that compounds containing sulfur (S) are an important source of endogenous acid production. In the metabolism, S is oxidized to sulfate, and therefore the mEq sulfate excreted in the urine is counted as acid retained in the body. In this study we show that pH in fluids with constant [Na] and [HEPES] declines as sulfate ions are added, and we show that titratable acidity increases exactly with the equivalents of sulfate. Therefore, sulfate excretion in urine is also acid excretion per se. This is in accordance with the down-regulation of proximal sulfate reabsorption under acidosis and the observation that children with distal renal tubular acidosis may be sulfate depleted. These results are well explained using charge-balance modeling, which is based only on the three fundamental principles of electroneutrality, conservation of mass, and rules of dissociation as devised from physical chemistry. In contrast, the findings are in contrast to expectations from conventional narratives. These are unable to understand the decreasing pH as sulfate is added since no conventional acid is present. The results may undermine the traditional notion of endogenous acid production since in the case of sulfur balance, S oxidation and its excretion as sulfate exactly balance each other. Possible clinical correlates with these findings are discussed.

Engineering the Thermodynamic Stability and Metastability of Mesophases of Colloidal Bipyramids through Shape Entropy

We report several types of entropy-driven phase transition behaviors in hard bipyramid systems using Monte Carlo simulations. Bipyramidal nanoparticle shapes are synthesizable from gold and silver, with sizes ranging from tens to hundreds of nanometers. We report numerous colloidal crystalline phases with varying symmetries and complexities as the bipyramid aspect ratio and base polygon are varied. Some bipyramids are mesogenic and undergo either monotropic or enantiotropic phase transitions. We show that such mesophase behavior can be modulated by tuning the bipyramid aspect ratio. In addition, we report stepwise kinetic crystallization and melting pathways that occur via an intermediate mesophase as the system gains or loses order in successive stages. Our results demonstrate that complex phase transition behavior involving mesophases can be driven by entropy alone. Importantly, our results can guide the synthesis of bipyramid shapes able to assemble target structures and can be used to engineer the kinetic pathways to and from those structures to involve or avoid mesophases.

Direct Imaging of the Kinetic Crystallization Pathway: Simulation and Liquid-Phase Transmission Electron Microscopy Observations

The crystallization of materials from a suspension determines the structure and function of the final product, and numerous pieces of evidence have pointed out that the classical crystallization pathway may not capture the whole picture of the crystallization pathways. However, visualizing the initial nucleation and further growth of a crystal at the nanoscale has been challenging due to the difficulties of imaging individual atoms or nanoparticles during the crystallization process in solution. Recent progress in nanoscale microscopy had tackled this problem by monitoring the dynamic structural evolution of crystallization in a liquid environment. In this review, we summarized several crystallization pathways captured by the liquid-phase transmission electron microscopy technique and compared the observations with computer simulation. Apart from the classical nucleation pathway, we highlight three nonclassical pathways that are both observed in experiments and computer simulations: formation of an amorphous cluster below the critical nucleus size, nucleation of the crystalline phase from an amorphous intermediate, and transition between multiple crystalline structures before achieving the final product. Among these pathways, we also highlight the similarities and differences between the experimental results of the crystallization of single nanocrystals from atoms and the assembly of a colloidal superlattice from a large number of colloidal nanoparticles. By comparing the experimental results with computer simulations, we point out the importance of theory and simulation in developing a mechanistic approach to facilitate the understanding of the crystallization pathway in experimental systems. We also discuss the challenges and future perspectives for investigating the crystallization pathways at the nanoscale with the development of in situ nanoscale imaging techniques and potential applications to the understanding of biomineralization and protein self-assembly.

The Antidepressant Paroxetine Reduces the Cardiac Sodium Current

A considerable amount of literature has been published on antidepressants and cardiac ion channel dysfunction. The antidepressant paroxetine has been associated with Brugada syndrome and long QT syndrome, albeit on the basis of conflicting findings. The cardiac voltage-gated sodium channel (Na_V1.5) is related to both of these syndromes, suggesting that paroxetine may have an effect on this channel. In the present study, we therefore carried out patch clamp experiments to examine the effect of paroxetine on human Na_V1.5 channels stably expressed in human embryonic kidney 293 (HEK-293) cells as well as on action potentials of isolated rabbit left ventricular cardiomyocytes. Additionally, computer simulations were conducted to test the functional effects of the experimentally observed paroxetine-induced changes in the Na_V1.5 current. We found that paroxetine led to a decrease in peak Na_V1.5 current in a concentration-dependent manner with an IC₅₀ of 6.8 ± 1.1 µM. In addition, paroxetine caused a significant hyperpolarizing shift in the steady-state inactivation of the Na_V1.5 current as well as a significant increase in its rate of inactivation. Paroxetine (3 µM) affected the action potential of the left ventricular cardiomyocytes, significantly decreasing its maximum upstroke velocity and amplitude, both of which are mainly regulated by the Na_V1.5 current. Our computer simulations demonstrated that paroxetine substantially reduces the fast sodium current of human left ventricular cardiomyocytes, thereby slowing conduction and reducing excitability in strands of cells, in particular if conduction and excitability are already inhibited by a loss-of-function mutation in the Na_V1.5 encoding SCN5A gene. In conclusion, paroxetine acts as an inhibitor of Na_V1.5 channels, which may enhance the effects of loss-of-function mutations in SCN5A.

Neural simulation pipeline: Enabling container-based simulations on-premise and in public clouds

In this study, we explore the simulation setup in computational neuroscience. We use GENESIS, a general purpose simulation engine for sub-cellular components and biochemical reactions, realistic neuron models, large neural networks, and system-level models. GENESIS supports developing and running computer simulations but leaves a gap for setting up today's larger and more complex models. The field of realistic models of brain networks has overgrown the simplicity of earliest models. The challenges include managing the complexity of software dependencies and various models, setting up model parameter values, storing the input parameters alongside the results, and providing execution statistics. Moreover, in the high performance computing (HPC) context, public cloud resources are becoming an alternative to the expensive on-premises clusters. We present Neural Simulation Pipeline (NSP), which facilitates the large-scale computer simulations and their deployment to multiple computing infrastructures using the infrastructure as the code (IaC) containerization approach. The authors demonstrate the effectiveness of NSP in a pattern recognition task programmed with GENESIS, through a custom-built visual system, called RetNet(8 × 5,1) that uses biologically plausible Hodgkin-Huxley spiking neurons. We evaluate the pipeline by performing 54 simulations executed on-premise, at the Hasso Plattner Institute's (HPI) Future Service-Oriented Computing (SOC) Lab, and through the Amazon Web Services (AWS), the biggest public cloud service provider in the world. We report on the non-containerized and containerized execution with Docker, as well as present the cost per simulation in AWS. The results show that our neural simulation pipeline can reduce entry barriers to neural simulations, making them more practical and cost-effective.

Phase Diagrams of Polymerization-Induced Self-Assembly Are Largely Determined by Polymer Recombination

In the current work, atom transfer radical polymerization-induced self-assembly (ATRP PISA) phase diagrams were obtained by the means of dissipative particle dynamics simulations. A fast algorithm for determining the equilibrium morphology of block copolymer aggregates was developed. Our goal was to assess how the chemical nature of ATRP affects the self-assembly of diblock copolymers in the course of PISA. We discovered that the chain growth termination via recombination played a key role in determining the ATRP PISA phase diagrams. In particular, ATRP with turned off recombination yielded a PISA phase diagram very similar to that obtained for a simple ideal living polymerization process. However, an increase in the recombination probability led to a significant change of the phase diagram: the transition between cylindrical micelles and vesicles was strongly shifted, and a dependence of the aggregate morphology on the concentration was observed. We speculate that this effect occurred due to the simultaneous action of two factors: the triblock copolymer architecture of the terminated chains and the dispersity of the solvophobic blocks. We showed that these two factors affected the phase diagram weakly if they acted separately; however, their combination, which naturally occurs during ATRP, affected the ATRP PISA phase diagram strongly. We suggest that the recombination reaction is a key factor leading to the complexity of experimental PISA phase diagrams.

Acetylcholine Reduces L-Type Calcium Current without Major Changes in Repolarization of Canine and Human Purkinje and Ventricular Tissue

Vagal nerve stimulation (VNS) holds a strong basis as a potentially effective treatment modality for chronic heart failure, which explains why a multicenter VNS study in heart failure with reduced ejection fraction is ongoing. However, more detailed information is required on the effect of acetylcholine (ACh) on repolarization in Purkinje and ventricular cardiac preparations to identify the advantages, risks, and underlying cellular mechanisms of VNS. Here, we studied the effect of ACh on the action potential (AP) of canine Purkinje fibers (PFs) and several human ventricular preparations. In addition, we characterized the effects of ACh on the L-type Ca²⁺ current (I_CaL) and AP of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and performed computer simulations to explain the observed effects. Using microelectrode recordings, we found a small but significant AP prolongation in canine PFs. In the human myocardium, ACh slightly prolonged the AP in the midmyocardium but resulted in minor AP shortening in subepicardial tissue. Perforated patch-clamp experiments on hiPSC-CMs demonstrated that 5 µM ACh caused an ≈15% decrease in I_CaL density without changes in gating properties. Using dynamic clamp, we found that under blocked K⁺ currents, 5 µM ACh resulted in an ≈23% decrease in AP duration at 90% of repolarization in hiPSC-CMs. Computer simulations using the O'Hara-Rudy human ventricular cell model revealed that the overall effect of ACh on AP duration is a tight interplay between the ACh-induced reduction in I_CaL and ACh-induced changes in K⁺ currents. In conclusion, ACh results in minor changes in AP repolarization and duration of canine PFs and human ventricular myocardium due to the concomitant inhibition of inward I_CaL and outward K⁺ currents, which limits changes in net repolarizing current and thus prevents major changes in AP repolarization.

Swelling and Collapse of Cylindrical Polyelectrolyte Microgels

In this study, we propose computer simulations of charged cylindrical microgels. The effects of cross-linking density, aspect ratio, and fraction of charged groups on the microgel swelling and collapse with a variation in the solvent quality were studied. The results were compared with those obtained for equivalent neutral cylindrical microgels. The study demonstrated that microgels' degree of swelling strongly depends on the fraction of charged groups. Polyelectrolyte microgels under adequate solvent conditions are characterized by a larger length and thickness than their neutral analogues: the higher the fraction of charged groups, the longer their length and greater their thickness. Microgels' collapse upon solvent quality decline is characterized by a decrease in length and non-monotonous behavior of its thickness. First, the thickness decreases due to the attraction of monomer units (beads) upon collapse. The further thickness increase is related to the surface tension, which tends to reduce the anisotropy of collapsed objects (the minimum surface energy is known to be achieved for the spherical objects). This reduction is opposed by the network elasticity. The microgels with a low cross-linking density and/or a low enough aspect ratio reveal a cylinder-to-sphere collapse. Otherwise, the cylindrical shape is preserved in the course of the collapse. Aspect ratio as a function of the solvent quality (interaction parameter) demonstrates the maximum, which is solely due to the electrostatics. Finally, we plotted radial concentration profiles for network segments, their charged groups, and counterions.

Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles

Cell-free protein synthesis is an important tool for studying gene expression and harnessing it for applications. In cells, gene expression is regulated in part by the spatial organization of transcription and translation. Unfortunately, current cell-free approaches are unable to control the organization of molecular components needed for gene expression, which limits the ability to probe and utilize its effects. Here, we show, using complementary computational and experimental approaches, that macromolecular crowding can be used to control the spatial organization and translational efficiency of gene expression in cell-sized vesicles. Computer simulations and imaging experiments reveal that, as crowding is increased, DNA plasmids become localized at the inner surface of vesicles. Ribosomes, in contrast, remain uniformly distributed, demonstrating that crowding can be used to differentially organize components of gene expression. We further carried out cell-free protein synthesis reactions in cell-sized vesicles and quantified mRNA and protein abundance. At sufficiently high levels of crowding, we observed localization of mRNA near vesicle surfaces, a decrease in translational efficiency and protein abundance, and anomalous scaling of protein abundance as a function of vesicle size. These results are consistent with high levels of crowding causing altered spatial organization and slower diffusion. Our work demonstrates a straightforward way to control the organization of gene expression in cell-sized vesicles and provides insight into the spatial regulation of gene expression in cells.

Energy Absorption Characteristics of Polygonal Bio-Inspired Honeycomb Column Thin-Walled Structure under Quasi-Static Uniaxial Compression Loading

In this paper, we investigated the internal structure of the beetle elytra, i.e., two different structural forms I and II of the bio-inspired honeycomb column thin-walled structures (BHTS) that give the honeycomb sandwich structure frequently used in construction projects better mechanical properties and lightweight performance. BHTS specimens were fabricated by additive manufacturing selective laser melting (AM-SLM) using AlSi10Mg Al-Si alloy. In order to understand the effect of section angle number on BHTS during loading, quasi-static uniaxial compression tests were carried out and verified by numerical simulation. The experimental results showed that in the quasi-static uniaxial compression tests, the number of section angles greatly improved the energy absorption (EA) index of each BHTS: the average value of initial peak crushing force (PCF) of hexagonal BHTS increased by 108.82% and 43.44%, respectively, compared to triangular and rectangular BHTS. The average value of the mean crushing force (MCF) increased by 74.87% and 45.48%, respectively. The average value of EA increased by 89.02% and 46.64%, respectively. The results indicate that the number of section angles can be used as an effective way to enhance the EA of BHTS. This work can provide a reference for the design of high-efficiency energy absorbers and will be widely used in EA scenarios such as construction, transportation, etc.

Computer Simulations of Silicide-Tetrahedrite Thermoelectric Generators

With global warming and rising energy demands, it is important now than ever to transit to renewable energy systems. Thermoelectric (TE) devices can present a feasible alternative to generate clean energy from waste heat. However, to become attractive for large-scale applications, such devices must be cheap, efficient, and based on ecofriendly materials. In this study, the potential of novel silicide-tetrahedrite modules for energy generation was examined. Computer simulations based on the finite element method (FEM) and implicit finite difference method (IFDM) were performed. The developed computational models were validated against data measured on a customized system working with commercial TE devices. The models were capable of predicting the TEGs' behavior with low deviations (≤10%). IFDM was used to study the power produced by the silicide-tetrahedrite TEGs for different ΔT between the sinks, whereas FEM was used to study the temperature distributions across the testing system in detail. To complement these results, the influence of the electrical and thermal contact resistances was evaluated. High thermal resistances were found to affect the devices ΔT up to ~15%, whereas high electrical contact resistances reduced the power output of the silicide-tetrahedrite TEGs by more than ~85%.

When Is a Potassium Channel Not a Potassium Channel?

Ever since they were first observed in Purkinje fibers of the heart, funny channels have had close connections to potassium channels. Indeed, funny channels were initially thought to produce a potassium current in the heart called I _K2. However, funny channels are completely unlike potassium channels in ways that make their contributions to the physiology of cells unique. An important difference is the greater ability for sodium to permeate funny channels. Although it does not flow through the funny channel as easily as does potassium, sodium does permeate well enough to allow for depolarization of cells following a strong hyperpolarization. This is critical for the function of funny channels in places like the heart and brain. Computational analyses using recent structures of the funny channels have provided a possible mechanism for their unusual permeation properties.

An Electrical Contacts Study for Tetrahedrite-Based Thermoelectric Generators

High electrical and thermal contact resistances can ruin a thermoelectric device's performance, and thus, the use of effective diffusion barriers and optimization of joining methods are crucial to implement them. In this work, the use of carbon as a Cu₁₁Mn₁Sb₄S₁₃ tetrahedrite diffusion barrier, and the effectiveness of different fixation techniques for the preparation of tetrahedrite/copper electrical contacts were investigated. Contacts were prepared using as jointing materials Ni and Ag conductive paints and resins, and a Zn-5wt% Al solder. Manual, cold- and hot-pressing fixation techniques were explored. The contact resistance was measured using a custom-made system based on the three points pulsed-current method. The legs interfaces (Cu/graphite/tetrahedrite) were investigated by optical and scanning electron microscopies, complemented with energy-dispersive X-ray spectroscopy, and X-ray diffraction. No interfacial phases were formed between the graphite and the tetrahedrite or Cu, pointing to graphite as a good diffusion barrier. Ag water-based paint was the best jointing material, but the use of hot pressing without jointing materials proves to be the most reliable technique, presenting the lowest contact resistance values. Computer simulations using the COMSOL software were performed to complement this study, indicating that high contact resistances strongly reduce the power output of thermoelectric devices.

Changes in Ion Concentrations upon the Binding of Short Polyelectrolytes on Phospholipid Bilayers: Computer Study Addressing Interesting Physiological Consequences

This computer study was inspired by the experimental observation of Y. Qian et al. published in ACS Applied Materials and Interfaces, 2018 that the short positively charged β-peptide chains and their oligomeric analogues efficiently suppress severe medical problems caused by antimicrobial drug-resistant bacteria despite them not penetrating the bacterial membrane. Our coarse-grained molecular dynamics (dissipative particle dynamics) simulations confirm the tentative explanation of the authors of the experimental study that the potent antimicrobial activity is a result of the entropically driven release of divalent ions (mainly magnesium ions essential for the proper biological function of bacteria) into bulk solution upon the electrostatic binding of β-peptides to the bacterial membrane. The study shows that in solutions containing cations Na⁺, Ca²⁺ and Mg²⁺, and anions Cl⁻, the divalent cations preferentially concentrate close to the membrane and neutralize the negative charge. Upon the addition of positively charged oligomer chains (models of β-peptides and their analogues), the oligomers electrostatically bind to the membrane replacing divalent ions, which are released into bulk solvent. Our simulations indicate that the entropy of small ions (which controls the behavior of synthetic polyelectrolyte solutions) plays an important role in this and also in other similar biologically important systems.

Endothelial glycocalyx permeability for nanoscale solutes

Glycocalyx has a great impact on the accessibility of the endothelial cell membranes. Although the specific interactions play a crucial role in cross-membrane solute transport, nonspecific interactions cannot be neglected. In this work, we used computational modeling to quantify the nonspecific interactions that control the distribution of nanosized solutes across the endothelial glycocalyx. We evaluated the probabilities of various nanoparticles' passage through the luminal layer to the membrane. The calculations demonstrate that excluded volume and electrostatic interactions are decisive for the solute transport as compared with van der Waals and hydrodynamic interactions. Damaged glycocalyx models showed a relatively weak efficiency in sieving plasma solutes. We estimated the energy barriers and corresponding mean first passage times for nanoscale solute transport through the model glycocalyx.

Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety

Antibiotics are often used in human and veterinary medicine for the treatment of bacterial diseases. However, extensive use of antibiotics in agriculture can result in the contamination of common food staples such as milk. Consumption of contaminated products can cause serious illness and a rise in antibiotic resistance. Conventional methods of antibiotics detection such are microbiological assays chromatographic and mass spectroscopy methods are sensitive; however, they require qualified personnel, expensive instruments, and sample pretreatment. Biosensor technology can overcome these drawbacks. This review is focused on the recent achievements in the electrochemical biosensors based on nucleic acid aptamers for antibiotic detection. A brief explanation of conventional methods of antibiotic detection is also provided. The methods of the aptamer selection are explained, together with the approach used for the improvement of aptamer affinity by post-SELEX modification and computer modeling. The substantial focus of this review is on the explanation of the principles of the electrochemical detection of antibiotics by aptasensors and on recent achievements in the development of electrochemical aptasensors. The current trends and problems in practical applications of aptasensors are also discussed.

Computer simulations of self-assembly of anisotropic colloids

Computer simulations have played a significant role in understanding the physics of colloidal self-assembly, interpreting experimental observations, and predicting novel mesoscopic and crystalline structures. Recent advances in computer simulations of colloidal self-assembly driven by anisotropic or orientation-dependent inter-particle interactions are highlighted in this review. These interactions are broadly classified into two classes: entropic and enthalpic interactions. They mainly arise due to shape anisotropy, surface heterogeneity, compositional heterogeneity, external field, interfaces, and confinements. Key challenges and opportunities in the field are discussed.

On the theory of synchrotron radiation nanofocusing with planar compound refractive lenses

Two new methods of computer simulation of synchrotron radiation nanofocusing with planar compound refractive lenses (PCRLs) are presented. The methods are based on the results of analytical theory. In contrast to previous works, the new methods take into account the PCRL aperture. It is especially important at high photon energies, when absorption is low and the calculations based on analytical theory, i.e. without taking into account the aperture, give incorrect results. A computer program was created and specific results were obtained for a silicon PCRL having an aperture of 50 µm, element length of 102 µm and minimum thickness of 2 µm. For an energy of 50 keV and number of elements 300, it focuses the beam to 31 nm size at a distance of one and a half times its length. Analysis of the calculation accuracy for the proposed methods is performed, as well as a demonstration of the capabilities of the computer program.

Implementation and Evaluation of a Virtual Reality Simulation: Intravenous Injection Training System

In nursing education, virtual reality simulation (VRS) is recognized as an effective learning method as it overcomes limitations in practical training and positively influences learning ability and satisfaction levels. The purpose of this study was to develop VRS for intravenous (IV) injection and investigate how it affects nursing students’ academic knowledge, performance confidence, and clinical practice competencies. A quasi-experimental control group pretest and post-test design was used. Participants were nursing students who either received a training system for an IV injection through VRS (experimental group; n = 20) or who received an IV arm simulator (control group; n = 20). The results revealed significantly higher knowledge (U = 156.5, p = 0.024) and clinical performance competency (U = 87.5, p = 0.002) with the procedure of using a training system of VRS for IV injection compared to having training via an IV arm simulator. This study verified that VRS for IV injection was more effective than an IV arm simulator for practical training on IV injection. Thus, VRS for IV injection, an effective teaching method used to improve learning ability and satisfaction levels, can be used as a training method in the future.

Challenging ancient DNA results about putative HLA protection or susceptibility to Yersina pestis

In a recent article, Immel et al. (Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, et al. 2021. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol. 38:4059–4076) extracted DNA from 36 individuals dead from plague in Ellwangen, Southern Germany, during the 16th century. By comparing their human leukocyte antigen (HLA) genotypes with those of 50 present-day Ellwangen inhabitants, the authors reported a significant decrease of HLA-B*51:01 and HLA-C*06:02 and a significant increase of HLA-DRB1*13:01/13:02 frequencies from ancient to modern populations. After comparing these frequencies with a larger sample of 8,862 modern Germans and performing simulations of natural selection, they concluded that these changes had been driven by natural selection. In an attempt to provide more evidence on such stimulating results, we explored the HLA frequency patterns over all of Europe, we predicted binding affinities of HLA-B/C/DRB1 alleles to 106,515 Yersinia pestis-derived peptides, and we performed forward simulations of HLA genetic profiles under neutrality. Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA.

Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states

The mammalian genome has a complex, functional 3D organization. However, it remains largely unknown how DNA contacts are orchestrated by chromatin organizers. Here, we infer from only Hi-C the cell-type-specific arrangement of DNA binding sites sufficient to recapitulate, through polymer physics, contact patterns genome wide. Our model is validated by its predictions in a set of duplications at Sox9 against available independent data. The binding site types fall in classes that well match chromatin states from segmentation studies, yet they have an overlapping, combinatorial organization along chromosomes necessary to accurately explain contact specificity. The chromatin signatures of the binding site types return a code linking chromatin states to 3D architecture. The code is validated by extensive de novo predictions of Hi-C maps in an independent set of chromosomes. Overall, our results shed light on how 3D information is encrypted in 1D chromatin via the specific combinatorial arrangement of binding sites.

Milk β-casein as delivery systems for luteolin: Multi-spectroscopic, computer simulations, and biological studies

β-Casein, a highly amphiphilic calcium-sensitive phosphoprotein, has specific features that promote its application as a nanocarrier for hydrophobic bioactives. Luteolin is a flavonoid with rich biological activities existing in vegetables and fruits. It is important to understand the interaction of β-casein with luteolin for the development of β-casein-based delivery systems. Here, the interaction mode between luteolin and β-casein was investigated with multispectral techniques, computer simulation, and biological methods. The results demonstrated that luteolin could bind to β-casein spontaneously which is driven by hydrophobic interactions and statically quench the intrinsic fluorescence of β-casein. Molecular docking and molecular dynamics simulation showed that β-casein formed a stable complex with luteolin. It could be concluded that luteolin was encapsulated in β-casein micelles and exhibited higher antioxidant activity than luteolin alone. These results would be helpful to understand the interaction mechanism of luteolin with β-casein and indicated that β-casein micelles were very promising as delivery vehicles for luteolin. PRACTICAL APPLICATIONS: Adding bioactive compounds to food is an efficient method of functional food processing, and protein is an excellent natural carrier for these substances. β-Casein is a milk protein with a unique amphiphilic structure that makes it a natural nanocarrier for active ingredients. This study created β-casein nanocarriers and encapsulated luteolin based on the interaction mechanism between β-casein with luteolin. Luteolin encapsulated in β-casein micelles demonstrated higher antioxidant activity when compared to free luteolin. This research will provide useful data for the development of functional foods based on β-casein and luteolin in the food industry.

The generalized continuous multiple step (GCMS) potential: model systems and benchmarks

The generalized continuous multiple step (GCMS) potential is presented in this work. Its flexible form allows forrepulsiveand/orattractivecontributions to be encoded through adjustable energy and length scales. The GCMS interaction provides a continuous representation of square-well, square-shoulder potentials and their variants for implementation in computer simulations. A continuous and differentiable energy representation is required to derive forces in conventional simulation algorithms. Molecular dynamics simulations are of particular interest when considering the dynamic properties of a system. The GCMS potential can mimic other interactions with a judicious choice of parameters due to the versatile sigmoid form. In this study, our benchmarks for the GCMS representation include triangular, Yukawa, Franzese, and Lennard-Jones potentials. Comparisons made with published data on volumetric phase diagrams, liquid structure, and diffusivity from model systems are in excellent agreement.

Numerical method to characterise capsule membrane permeability for controlled drug delivery

Design and characterisation of capsules is not an easy task owing to the multiple involved preparation factors and parameters. Here, a novel method to characterise capsule membrane permeability to solute molecules by an inverse approach is proposed. Transport of chemical species between the capsule core and the surrounding medium through the membrane is described by the Fick's second law with a position-dependent diffusion coefficient. Solutions are computed in spherical coordinates using a finite difference scheme developed for diffusion in multilayer configuration. They are validated using semi-analytical solutions and fully three-dimensional lattice Boltzmann simulations. As a proof of concept, the method is applied to experimental data available in the literature on the kinetics of glucose release and absorption to determine the membrane permeability of capsules. The proposed method is easy to use and determines correctly the permeability of capsule membranes for controlled drug release and absorption applications.

A review of advances in tribology in 2020–2021

Around 1,000 peer-reviewed papers were selected from 3,450 articles published during 2020–2021, and reviewed as the representative advances in tribology research worldwide. The survey highlights the development in lubrication, wear and surface engineering, biotribology, high temperature tribology, and computational tribology, providing a show window of the achievements of recent fundamental and application researches in the field of tribology.

Cargo Release from Nonenveloped Viruses and Virus-like Nanoparticles: Capsid Rupture or Pore Formation

Virus-like nanoparticles are protein shells similar to wild-type viruses, and both aim to deliver their content into a cell. Unfortunately, the release mechanism of their cargo/genome remains elusive. Pores on the symmetry axes were proposed to enable the slow release of the viral genome. In contrast, cryo-EM images showed that capsids of nonenveloped RNA viruses can crack open and rapidly release the genome. We combined in vitro cryo-EM observations of the genome release of three viruses with coarse-grained simulations of generic virus-like nanoparticles to investigate the cargo/genome release pathways. Simulations provided details on both slow and rapid release pathways, including the success rates of individual releases. Moreover, the simulated structures from the rapid release pathway were in agreement with the experiment. Slow release occurred when interactions between capsid subunits were long-ranged, and the cargo/genome was noncompact. In contrast, rapid release was preferred when the interaction range was short and/or the cargo/genome was compact. These findings indicate a design strategy of virus-like nanoparticles for drug delivery.

Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars

This computational study investigates the influence of light on supramolecular aggregates of three-arm azobenzene stars. Every star contains three azobenzene (azo) moieties, each able to undergo reversible photoisomerization. In solution, the azo stars build column-shaped supramolecular aggregates. Previous experimental works report severe morphological changes of these aggregates under UV-Vis light. However, the underlying molecular mechanisms are still debated. Here we aim to elucidate how light affects the structure and stability of the columnar stacks on the molecular scale. The system is investigated using fully atomistic molecular dynamics (MD) simulations. To implement the effects of light, we first developed a stochastic model of the cyclic photoisomerization of azobenzene. This model reproduces the collective photoisomerization kinetics of the azo stars in good agreement with theory and previous experiments. We then apply light of various intensities and wavelengths on an equilibrated columnar stack of azo stars in water. The simulations indicate that the aggregate does not break into separate fragments upon light irradiation. Instead, the stack develops defects in the form of molecular shifts and reorientations and, as a result, it eventually loses its columnar shape. The mechanism and driving forces behind this order-disorder structural transition are clarified based on the simulations. In the end, we provide a new interpretation of the experimentally observed morphological changes.

Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations

We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of π-π interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the π-π interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, π-π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.

Toward enzyme-responsive polymersome drug delivery

In drug delivery, enzyme-responsive drug carriers are becoming increasingly relevant because of the growing association of disease pathology with enzyme overexpression. Polymersomes are of interest to such applications because of their tunable properties. While polymersomes open up a wide range of chemical and physical properties to explore, they also present a challenge in developing generalized rules for the synthesis of novel systems. Motivated by this issue, in this perspective, we summarize the existing knowledge on enzyme-responsive polymersomes and outline the main design choices. Then, we propose heuristics to guide the design of novel systems. Finally, we discuss the potential of an integrated approach using computer simulations and experimental studies to streamline this design process and close the existing knowledge gaps.