Nanoconfinement of Carbon Dioxide within Interfacial Aqueous/Ionic Liquid Systems.

Nanoporous, gas-selective membranes have shown encouraging results for the removal of CO2 from flue gas, yet the optimal design for such membranes is often unknown. Therefore, we used molecular dynamics simulations to elucidate the behavior of CO2 within aqueous and ionic liquid (IL) systems ([EMIM][TFSI] and [OMIM][TFSI]), both confined individually and as an interfacial aqueous/IL system. We found that within aqueous systems the mobility of CO2 is reduced due to interactions between the CO2 oxygens and hydroxyl groups on the pore surface. Within the IL systems, we found that confinement has a greater effect on the [EMIM][TFSI] system as opposed to the [OMIM][TFSI] system. Paradoxically, the larger and more asymmetrical [OMIM]+ molecule undergoes less efficient packing, resulting in fewer confinement effects. Free energy surfaces of the nanoconfined aqueous/IL interface demonstrate that CO2 will transfer spontaneously from the aqueous to the IL phase.

Erratum: Addition to "Carbonic Anhydrase Robustness for Use in Nanoscale CO2 Capture Technologies".

[This corrects the article DOI: 10.1021/acsomega.3c02630.].

Cohort profile: evaluation of immune response and household transmission of SARS-CoV-2 in Costa Rica: the RESPIRA study.

PURPOSE: The RESPIRA cohort aims to describe the nature, magnitude, time course and efficacy of the immune response to SARS-CoV-2 infection and vaccination, population prevalence, and household transmission of COVID-19. PARTICIPANTS: From November 2020, we selected age-stratified random samples of COVID-19 cases from Costa Rica confirmed by PCR. For each case, two population-based controls, matched on age, sex and census tract were recruited, supplemented with hospitalised cases and household contacts. Participants were interviewed and blood and saliva collected for antibodies and PCR tests. Participants will be followed for 2 years to assess antibody response and infection incidence. FINDINGS TO DATE: Recruitment included 3860 individuals: 1150 COVID-19 cases, 1999 population controls and 719 household contacts from 304 index cases. The age and regional distribution of cases was as planned, including four age strata, 30% rural and 70% urban. The control cohort had similar sex, age and regional distribution as the cases according to the study design. Among the 1999 controls recruited, 6.8% reported at enrolment having had COVID-19 and an additional 12.5% had antibodies against SARS-CoV-2. Compliance with visits and specimens has been close to 70% during the first 18 months of follow-up. During the study, national vaccination was implemented and nearly 90% of our cohort participants were vaccinated during follow-up. FUTURE PLANS: RESPIRA will enable multiple analyses, including population prevalence of infection, clinical, behavioural, immunological and genetic risk factors for SARS-CoV-2 acquisition and severity, and determinants of household transmission. We are conducting retrospective and prospective assessment of antibody levels, their determinants and their protective efficacy after infection and vaccination, the impact of long-COVID and a series of ancillary studies. Follow-up continues with bimonthly saliva collection for PCR testing and biannual blood collection for immune response analyses. Follow-up will be completed in early 2024. TRIAL REGISTRATION NUMBER: NCT04537338.

Transport and Energetics of Carbon Dioxide in Ionic Liquids at Aqueous Interfaces.

A major hurdle in utilizing carbon dioxide (CO2) lies in separating it from industrial flue gas mixtures and finding suitable storage methods that enable its application in various industries. To address this issue, we utilized a combination of molecular dynamics simulations and experiments to investigate the behavior of CO2 in common room-temperature ionic liquids (RTIL) when in contact with aqueous interfaces. Our investigation of RTILs, [EMIM][TFSI] and [OMIM][TFSI], and their interaction with a pure water layer mimics the environment of a previously developed ultrathin enzymatic liquid membrane for CO2 separation. We analyzed diffusion constants and viscosity, which reveals that CO2 molecules exhibit faster mobility within the selected ILs compared to what would be predicted solely based on the viscosity of the liquids using the standard Einstein-Stokes relation. Moreover, we calculated the free energy of translocation for various species across the aqueous-IL interface, including CO2 and HCO3-. Free energy profiles demonstrate that CO2 exhibits a more favorable partitioning behavior in the RTILs compared to that in pure water, while a significant barrier hinders the movement of HCO3- from the aqueous layer. Experimental measurement of the CO2 transport in the RTILs corroborates the model. These findings strongly suggest that hydrophobic RTILs could serve as a promising option for selectively transporting CO2 from aqueous media and concentrating it as a preliminary step toward storage.

Energetics of high temperature degradation of fentanyl into primary and secondary products.

Fentanyl is a synthetic opioid used for managing chronic pain. Due to its higher potency (50-100×) than morphine, fentanyl is also an abused drug. A sensor that could detect illicit fentanyl by identifying its thermally degraded fragments would be helpful to law enforcement. While experimental studies have probed the thermal degradation of fentanyl, little theoretical work has been done to understand the mechanism. Here, we studied the thermal degradation pathways of fentanyl using extensive ab initio molecular dynamics simulations combined with enhanced sampling via multiple-walker metadynamics. We calculated the free energy profile for each bond suggested earlier as a potential degradation point to map the thermodynamic driving forces. We also estimated the forward attempt rate of each bond degradation reaction to gain information about degradation kinetics.

Carbonic Anhydrase Robustness for Use in Nanoscale CO2 Capture Technologies.

Continued dependence on crude oil and natural gas resources for fossil fuels has caused global atmospheric carbon dioxide (CO2) emissions to increase to record-setting proportions. There is an urgent need for efficient and inexpensive carbon sequestration systems to mitigate large-scale emissions of CO2 from industrial flue gas. Carbonic anhydrase (CA) has shown high potential for enhanced CO2 capture applications compared to conventional absorption-based methods currently utilized in various industrial settings. This study aims to understand structural aspects that contribute to the stability of CA enzymes critical for their applications in industrial processes, which require the ability to withstand conditions different from those in their native environments. Here, we evaluated the thermostability and enzyme activity of mesophilic and thermophilic CA variants at different temperature conditions and in the presence of atmospheric gas pollutants like nitrogen oxides and sulfur oxides. Based on our enzyme activity assays and molecular dynamics simulations, we see increased conformational stability and CA activity levels in thermostable CA variants incubated week-long at different temperature conditions. The thermostable CA variants also retained high levels of CA activity despite changes in solution pH due to increasing NO and SO2 concentrations. A loss of CA activity was observed only at high concentrations of NO/SO2 that possibly can be minimized with the appropriate buffered solutions.

Membrane mediated mechanical stimuli produces distinct active-like states in the AT1 receptor.

The Angiotensin II Type 1 (AT1) receptor is one of the most widely studied GPCRs within the context of biased signaling. While the AT1 receptor is activated by agonists such as the peptide AngII, it can also be activated by mechanical stimuli such as membrane stretch or shear in the absence of a ligand. Despite the importance of mechanical activation of the AT1 receptor in biological processes such as vasoconstriction, little is known about the structural changes induced by external physical stimuli mediated by the surrounding lipid membrane. Here, we present a systematic simulation study that characterizes the activation of the AT1 receptor under various membrane environments and mechanical stimuli. We show that stability of the active state is highly sensitive to membrane thickness and tension. Structural comparison of membrane-mediated vs. agonist-induced activation shows that the AT1 receptor has distinct active conformations. This is supported by multi-microsecond free energy calculations that show unique landscapes for the inactive and various active states. Our modeling results provide structural insights into the mechanical activation of the AT1 receptor and how it may produce different functional outcomes within the framework of biased agonism.

The Dysferlin C2A Domain Binds PI(4,5)P2 and Penetrates Membranes.

Dysferlin is a large membrane protein found most prominently in striated muscle. Loss of dysferlin activity is associated with reduced exocytosis, abnormal intracellular Ca2+ and the muscle diseases limb-girdle muscular dystrophy and Miyoshi myopathy. The cytosolic region of dysferlin consists of seven C2 domains with mutations in the C2A domain at the N-terminus resulting in pathology. Despite the importance of Ca2+ and membrane binding activities of the C2A domain for dysferlin function, the mechanism of the domain remains poorly characterized. In this study we find that the C2A domain preferentially binds membranes containing PI(4,5)P2 through an interaction mediated by residues Y23, K32, K33, and R77 on the concave face of the domain. We also found that subsequent to membrane binding, the C2A domain inserts residues on the Ca2+ binding loops into the membrane. Analysis of solution NMR measurements indicate that the domain inhabits two distinct structural states, with Ca2+ shifting the population between states towards a more rigid structure with greater affinity for PI(4,5)P2. Based on our results, we propose a mechanism where Ca2+ converts C2A from a structurally dynamic, low PI(4,5)P2 affinity state to a high affinity state that targets dysferlin to PI(4,5)P2 enriched membranes through interaction with Tyr23, K32, K33, and R77. Binding also involves changes in lipid packing and insertion by the third Ca2+ binding loop of the C2 domain into the membrane, which would contribute to dysferlin function in exocytosis and Ca2+ regulation.

Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica.

INTRODUCTION: Variability in household secondary attack rates and transmission risks factors of SARS-CoV-2 remain poorly understood. METHODS: We conducted a household transmission study of SARS-CoV-2 in Costa Rica, with SARS-CoV-2 index cases selected from a larger prospective cohort study and their household contacts were enrolled. A total of 719 household contacts of 304 household index cases were enrolled from November 21, 2020, through July 31, 2021. Blood specimens were collected from contacts within 30-60 days of index case diagnosis; and serum was tested for presence of spike and nucleocapsid SARS-CoV-2 IgG antibodies. Evidence of SARS-CoV-2 prior infections among household contacts was defined based on the presence of both spike and nucleocapsid antibodies. We fitted a chain binomial model to the serologic data, to account for exogenous community infection risk and potential multi-generational transmissions within the household. RESULTS: Overall seroprevalence was 53% (95% confidence interval (CI) 48-58%) among household contacts. The estimated household secondary attack rate is 34% (95% CI 5-75%). Mask wearing by the index case is associated with the household transmission risk reduction by 67% (adjusted odds ratio = 0.33 with 95% CI: 0.09-0.75) and not sharing bedroom with the index case is associated with the risk reduction of household transmission by 78% (adjusted odds ratio = 0.22 with 95% CI 0.10-0.41). The estimated distribution of household secondary attack rates is highly heterogeneous across index cases, with 30% of index cases being the source for 80% of secondary cases. CONCLUSIONS: Modeling analysis suggests that behavioral factors are important drivers of the observed SARS-CoV-2 transmission heterogeneity within the household.

When living in the same house with known SARS-CoV-2 cases, household members may change their behavior and adopt preventive measures to reduce the spread of SARS-CoV-2. To understand how behavioral factors affect SARS-CoV-2 spreading in household settings, we focused on household members of individuals with laboratory-confirmed SARS-CoV-2 infections and followed the way SARS-CoV-2 spread within the household, by looking at who had antibodies against the virus, which means they were infected. We also asked participants detailed questions about their behavior and applied mathematical modeling to evaluate its impact on SARS-CoV-2 transmission. We found that mask-wearing by the SARS-CoV-2 cases, and avoiding sharing a bedroom with the infected individuals, reduces SARS-CoV-2 transmission. However, caring for SARS-CoV-2 cases, and prolonged interaction with infected individuals facilitate SARS-CoV-2 spreading. Our study helps inform what behaviors can help reduce SARS-CoV-2 transmission within a household.

Identification, Heterologous Expression, and Characterization of the Tolypodiol Biosynthetic Gene Cluster through an Integrated Approach.

Cyanobacteria are tremendous producers of biologically active natural products, including the potent anti-inflammatory compound tolypodiol. However, linking biosynthetic gene clusters with compound production in cyanobacteria has lagged behind that in other bacterial genera. Tolypodiol is a meroterpenoid originally isolated from the cyanobacterium HT-58-2. Here we describe the identification of the tolypodiol biosynthetic gene cluster through heterologous expression in Anabaena and in vitro protein assays of a methyltransferase found in the tolypodiol biosynthetic gene cluster. We have also identified similar biosynthetic gene clusters in cyanobacterial and actinobacterial genomes, suggesting that meroterpenoids with structural similarity to the tolypodiols may be synthesized by other microbes. We also report the identification of two new analogs of tolypodiol that we have identified in both the original and heterologous producer. This work further illustrates the usefulness of Anabaena as a heterologous expression host for cyanobacterial compounds and how integrated approaches can help to link natural product compounds with their producing biosynthetic gene clusters.

Tight hydrophobic core and flexible helices yield MscL with a high tension gating threshold and a membrane area mechanical strain buffer.

The mechanosensitive (MS) channel of large conductance, MscL, is the high-tension threshold osmolyte release valve that limits turgor pressure in bacterial cells in the event of drastic hypoosmotic shock. Despite MscL from Mycobacterium tuberculosis (TbMscL) being the first structurally characterized MS channel, its protective mechanism of activation at nearly-lytic tensions has not been fully understood. Here, we describe atomistic simulations of expansion and opening of wild-type (WT) TbMscL in comparison with five of its gain-of-function (GOF) mutants. We show that under far-field membrane tension applied to the edge of the periodic simulation cell, WT TbMscL expands into a funnel-like structure with trans-membrane helices bent by nearly 70°, but does not break its 'hydrophobic seal' within extended 20 µs simulations. GOF mutants carrying hydrophilic substitutions in the hydrophobic gate of increasing severity (A20N, V21A, V21N, V21T and V21D) also quickly transition into funnel-shaped conformations but subsequently fully open within 1-8 µs. This shows that solvation of the de-wetted (vapor-locked) constriction is the rate-limiting step in the gating of TbMscL preceded by area-buffering silent expansion. Pre-solvated gates in these GOF mutants reduce this transition barrier according to hydrophilicity and the most severe V21D eliminates it. We predict that the asymmetric shape-change of the periplasmic side of the channel during the silent expansion provides strain-buffering to the outer leaflet thus re-distributing the tension to the inner leaflet, where the gate resides.

Trends in incidence rates of head and neck squamous cell carcinomas overall and by potential relatedness to human papillomavirus, Costa Rica 2006 to 2015.

In Costa Rica (CR), only one report on head and neck cancer (HNC) incidence trends (1985-2007) has been published and no investigations on the epidemiology of potentially human papillomavirus (HPV)-related and HPV-unrelated HNCs have been done. We examined the age-standardized incidence rates (IRs) and trends of head and neck squamous cell carcinomas (HNSCC) and compared incidence trends of potentially HPV-related and HPV-unrelated HNSCCs. We obtained all available HNC cases for the period 2006-2015 from the Costa Rican National Cancer Registry of Tumors and the population estimates from the Costa Rican National Institute of Statistics and Census. The analysis was restricted to invasive HNSCCs (n = 1577). IRs and incidence rate ratios were calculated using SEER*Stat software and were age-standardized for the 2010 Costa Rican population. Joinpoint regression analysis program was used to calculate trends and annual percent changes (APCs) in rates. For all HNSCCs, the age-standardized IR was 34.0/million person-years; 95% CI 32.4, 35.8. There was a significant decline in the incidence of nasopharyngeal cancer (APC: -5.9% per year; 95% CI -10.8, -0.7) and laryngeal cancer (APC: -5.4% per year; -9.2, 1.5). The incidence trends for hypopharyngeal, oropharyngeal and oral cavity cancers each remained stable over time. HNSCCs were categorized by their potential relatedness to HPV infection. Though the APCs were not statistically significant, IRs of potentially HPV-related HNSCCs trended upward, while HPV-unrelated HNSCCs trended downward. HNSCCs are uncommon in CR and decreased over time. We observed a divergent pattern of decreasing HPV-unrelated with increasing HPV-related HNSCCs that should be further informed by HPV genotyping tumor samples.

Effect of Local Stress on Accurate Modeling of Bacterial Outer Membranes Using All-Atom Molecular Dynamics.

Biological membranes are fundamental components of living organisms that play an undeniable role in their survival. Molecular dynamics (MD) serves as an essential computational tool for studying biomembranes on molecular and atomistic scales. The status quo of MD simulations of biomembranes studies a nanometer-sized membrane patch periodically extended under periodic boundary conditions (PBCs). In nature, membranes are usually composed of different lipids in their two layers (referred to as leaflets). This compositional asymmetry imposes a fixed ratio of lipid numbers between the two leaflets in a periodically constrained membrane, which needs to be set appropriately. The widely adopted methods of defining a leaflet lipid ratio suffer from the lack of control over the mechanical tension of each leaflet, which could significantly influence research findings. In this study, we investigate the role of membrane-building protocol and the resulting initial stress state on the interaction between small molecules and asymmetric membranes. We model the outer membrane of Pseudomonas aeruginosa bacteria using two different building protocols and probe their interactions with the Pseudomonas quinolone signal (PQS). Our results show that differential stress could shift the position of free energy minimum for the PQS molecule between the two leaflets of the asymmetric membrane. This work provides critical insights into the relationship between the initial per-leaflet tension and the spontaneous intercalation of PQS.

Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica.

Variability in household secondary attack rates (SAR) and transmission risks factors of SARS-CoV-2 remain poorly understood. To characterize SARS-CoV-2 transmission in a household setting, we conducted a household serologic study of SARS-CoV-2 in Costa Rica, with SARS-CoV-2 index cases selected from a larger prospective cohort study and their household contacts were enrolled. A total of 719 household contacts of 304 household index cases were enrolled from November 21, 2020, through July 31, 2021. Demographic, clinical, and behavioral information was collected from the index cases and their household contacts. Blood specimens were collected from contacts within 30-60 days of index case diagnosis; and serum was tested for presence of spike and nucleocapsid SARS-CoV-2 IgG antibodies. Evidence of SARS-CoV-2 prior infections among household contacts was defined based on the presence of both spike and nucleocapsid antibodies. To avoid making strong assumptions that the index case was the sole source of infections among household contacts, we fitted a chain binomial model to the serologic data, which allowed us to account for exogenous community infection risk as well as potential multi-generational transmissions within the household. Overall seroprevalence was 53% (95% confidence interval (CI) 48% - 58%) among household contacts The estimated household secondary attack rate (SAR) was 32% (95% CI 5% - 74%) and the average community infection risk was 19% (95% CI 14% - 26%). Mask wearing by the index case was associated with the household transmission risk reduction by 67% (adjusted odds ratio = 0.33 with 95% CI: 0.09-0.75) and sleeping in a separate bedroom from the index case reduced the risk of household transmission by 78% (adjusted odds ratio = 0.22 with 95% CI 0.10-0.41). The estimated distribution of household secondary attack rates was highly heterogeneous across index cases, with 30% of index cases being the source for 80% of secondary cases. Modeling analysis suggests behavioral factors were important drivers of the observed SARS-CoV-2 transmission heterogeneity within the household.

Spinodal de-wetting of light liquids on graphene.

We demonstrate theoretically the possibility of spinodal de-wetting in heterostructures made of light-atom liquids (hydrogen, helium, and nitrogen) deposited on suspended graphene. Extending our theory of film growth on two-dimensional (2D) materials to include analysis of surface instabilities via the hydrodynamic Cahn-Hilliard-type equation, we characterize in detail the spatial and temporal scales of the resulting spinodal de-wetting patterns. Both linear stability analysis and direct numerical simulations of the surface hydrodynamics show micron-sized (generally material dependent) patterns of 'dry' regions. The physical reason for the development of such instabilities on graphene can be traced back to the inherently weak van der Waals interactions between atomically thin materials and atoms in the liquid. Thus 2D materials could represent a new theoretical and technological platform for studies of spinodal de-wetting.

Predictions of attrition among US Marine Corps: Comparison of four predictive methods.

The present study compared the performance of logistic regression models with that of machine learning classification models (classification trees and random forests) in the context of predicting training attrition from the Delayed Enlistment Program in the United States Marine Corps (USMC) with scores from the Tailored Adaptive Personality Assessment System (TAPAS). Performance was assessed according to the type of misclassification error and across a variety of different reasons for attrition. The base rate of attrition was low, which impeded the training process, but the machine learning models outperformed logistic regression in predicting voluntary attrition in a stratified 50% attrition sample.

Ciberdelincuencia en Colombia: ¿qué tan eficiente ha sido la Ley de Delitos Informáticos? / Cybercrime in Colombia: how efficient has the Computer Crime Law been? / Cibercrime na Colômbia: qual tem sido a eficácia da Lei de Crimes Informáticos?

Este documento está centrado en determinar qué variables afectan los incentivos que tienen los delincuentes al cometer sus ciberdelitos, e identificar si la legislación actual está diseñada teniendo en cuenta la tipificación de las conductas y las herramientas de los entes encargados de capturar los criminales. Se busca entender los principales factores que incentivan la ciberdelincuencia en el país, teniendo en cuenta el contexto de la ciberdelincuencia para el 2019 en Colombia, y con ello, el comportamiento de los delincuentes informáticos en la prepandemia. Con la Ley 1273 de 2019, encargada de tipificar los delitos informáticos en Colombia, se revisarán los datos reportados de delitos informáticos y se compararán con los casos e indicadores de delitos de hurto calificado, con el fin de determinar la relación de estos dos delitos, que son relevantes para las entidades y han sido interiorizados por las entidades policivas en su estudio y lucha anticriminal desde hace mucho tiempo. Una vez definida teóricamente la eficiencia de las entidades apoderadas en la lucha contra los delitos informáticos, se propone una función de beneficios económicos de la ciberdelincuencia adaptada para el caso colombiano, determinando las variables que mejor explican esta función. Al final de este ejercicio académico, mediante un análisis de sensibilidad, se señala qué aspectos de política pública se deben considerar como prioritarios, teniendo en cuenta los incentivos económicos para los ciberdelincuentes y la efectividad de la Ley 1273 de 2009.

This paper is focused on determining which variables affect the incentives that criminals have when committing cybercrime, and identify whether the current legislation is designed taking into account the criminalization of behaviors and the tools of the entities in charge of catching criminals. It seeks to understand the main factors that encourage cybercrime in the country, taking into account the context of cybercrime for 2019 in Colombia, and with it, the behavior of cybercriminals in the pre-pandemic. With Law 1273 of 2019, in charge of criminalizing computer crimes in Colombia, the reported data of computer crimes will be reviewed and compared with the cases and indicators of qualified theft crimes, in order to determine the relationship of these two crimes, which are relevant for the entities and have been internalized by the police entities in their study and anti-crime fight for a long time. Once the efficiency of the entities empowered in the fight against cybercrime has been theoretically defined, a function of economic benefits of cybercrime adapted to the Colombian case is proposed, determining the variables that best explain this function. At the end of this academic exercise, through a sensitivity analysis, it is pointed out which aspects of public policy should be considered as a priority, taking into account the economic incentives for cybercriminals and the effectiveness of Law 1273 of 2009.

Este documento está focado em determinar quais variáveis afetam os incentivos que os criminosos têm quando cometem crimes cibernéticos, e identificar se a legislação atual é elaborada levando em conta a classificação dos comportamentos e as ferramentas das entidades encarregadas de capturar os criminosos. Ela procura compreender os principais fatores que incentivam o cibercrime no país, levando em conta o contexto do cibercrime para 2019 na Colômbia, e com ele, o comportamento dos cibercriminosos na pré-pandemia. Com a Lei 1273 de 2019, encarregada de criminalizar os crimes cibernéticos na Colômbia, os dados comunicados de crimes cibernéticos serão revistos e comparados com os casos e indicadores de crimes de roubo, a fim de determinar a relação entre esses dois crimes, que são relevantes para as entidades e foram internalizados por entidades policiais em seu estudo e combate aos crimes por um longo tempo. Uma vez definida teoricamente a eficiência das entidades habilitadas na luta contra o crime cibernético, propõe-se uma função dos benefícios econômicos do crime cibernético adaptada ao caso colombiano, determinando as variáveis que melhor explicam esta função. Ao final deste exercício acadêmico, por meio de uma análise de sensibilidade, indica-se quais aspectos das políticas públicas devem ser considerados prioritários, levando em conta os incentivos econômicos para os cibercriminosos e a eficácia da Lei 1273 de 2009.

Mechanical Activation of MscL Revealed by a Locally Distributed Tension Molecular Dynamics Approach.

Membrane tension perceived by mechanosensitive (MS) proteins mediates cellular responses to mechanical stimuli and osmotic stresses, and it also guides multiple biological functions including cardiovascular control and development. In bacteria, MS channels function as tension-activated pores limiting excessive turgor pressure, with MS channel of large conductance (MscL) acting as an emergency release valve preventing cell lysis. Previous attempts to simulate gating transitions in MscL by either directly applying steering forces to the protein or by increasing the whole-system tension were not fully successful and often disrupted the integrity of the system. We present a novel, to our knowledge, locally distributed tension molecular dynamics (LDT-MD) simulation method that allows application of forces continuously distributed among lipids surrounding the channel using a specially constructed collective variable. We report reproducible and reversible transitions of MscL to the open state with measured parameters of lateral expansion and conductivity that exactly satisfy experimental values. The LDT-MD method enables exploration of the MscL-gating process with different pulling velocities and variable tension asymmetry between the inner and outer membrane leaflets. We use LDT-MD in combination with well-tempered metadynamics to reconstruct the tension-dependent free-energy landscape for the opening transition in MscL. The flexible definition of the LDT collective variable allows general application of our method to study mechanical activation of any membrane-embedded protein.

Balance of Solvent and Chain Interactions Determines the Local Stress State of Simulated Membranes.

Characterization of the internal mechanical state of model lipid membranes is essential to understand the microscopic underpinnings of biological functions such as membrane fission and organelle shaping within the context of elastic theories such as the Helfrich framework. Here, we compute lateral stress or pressure profiles from molecular dynamics simulations of lipid bilayers and water-vacuum interfaces to understand the role that solvent treatment and force-field parametrization plays on the local mechanical features of membranes. We focus on two atomistic models, GROMOS 43A1-S3 and CHARMM36, and several variants of the MARTINI coarse-grained force-field, including the single-bead nonpolar water, three-point polarizable water, big multipole water, and solvent-free variants. Our results show that the various atomistic and coarse-grained force-fields produce contrasting lateral stress profiles as a result of the balance of solvent-solvent and solvent-solute forces at the hydrocarbon-water interface and fundamentally different treatment of pairwise (e.g., van der Waals, Coulomb, etc.) and multibody interactions (angles and torsions). Numerical integration of the second moment of the bilayer stress profiles indicates that different local distributions of repulsive and attractive stresses across the membrane, due to distinct force-field parametrizations, may result in substantial variations in macroscopic elastic properties.