How a few help all: cooperative crossing of lipid membranes by COSAN anions.

Experimental results show that the presence of a concentration gradient of certain nano-ions (most notably cobaltabisdicarbollide ([o-COSAN]- anions), induce a current across intact artificial phospholipid bilayers in spite of the high Born free energy estimated for these ions. The mechanism underlying this observed translocation of nano-anions across membranes has yet to be determined. Here we show, using molecular dynamics simulations, that the permeation of [o-COSAN]- anions across a lipid bilayer proceeds in a cooperative manner. Single nano-ions can enter the bilayer but permeation is hampered by a free energy barrier of about 8kBT. The interaction between these nano-ions inside a leaflet induces a flip-flop translocation mechanism with the formation of transient, elongated structure inside the membrane. This cooperative flip-flop allows an efficient distribution of [o-COSAN]- anions in both leaflets of the bilayer. These results suggest the existence of a new mechanism for permeation of nano-ions across lipid membranes, relevant for those that have the appropriate self-assembly character.

MMS Observations of a Compressed Current Sheet: Importance of the Ambipolar Electric Field.

Spacecraft data reveal a nonuniform ambipolar electric field transverse to the magnetic field in a thin current sheet in Earth's magnetotail that leads to intense E×B velocity shear and nongyrotropic particle distributions. The E×B drift far exceeds the diamagnetic drift and thus drives observed lower hybrid waves. The shear-driven waves are localized to the magnetic field reversal region and are therefore ideally suited for the anomalous dissipation necessary for reconnection. It also reveals substructures embedded in the current density, indicating a compressed current sheet.

Cross-scale energy cascade powered by magnetospheric convection.

Plasma convection in the Earth's magnetosphere from the distant magnetotail to the inner magnetosphere occurs largely in the form of mesoscale flows, i.e., discrete enhancements in the plasma flow with sharp dipolarizations of magnetic field. Recent spacecraft observations suggest that the dipolarization flows are associated with a wide range of kinetic processes such as kinetic Alfvén waves, whistler-mode waves, and nonlinear time-domain structures. In this paper we explore how mesoscale dipolarization flows produce suprathermal electron instabilities, thus providing free energy for the generation of the observed kinetic waves and structures. We employ three-dimensional test-particle simulations of electron dynamics one-way coupled to a global magnetospheric model. The simulations show rapid growth of interchanging regions of parallel and perpendicular electron temperature anisotropies distributed along the magnetic terrain formed around the dipolarization flows. Unencumbered in test-particle simulations, a rapid growth of velocity-space anisotropies in the collisionless magnetotail plasma is expected to be curbed by the generation of plasma waves. The results are compared with in situ observations of an isolated dipolarization flow at one of the Magnetospheric Multiscale Mission spacecraft. The observations show strong wave activity alternating between broad-band wave activity and whistler waves. With estimated spatial extent being similar to the characteristic size of the temperature anisotropy patches in our test-particle simulations, the observed bursts of the wave activity are likely to be produced by the parallel and perpendicular electron energy anisotropies driven by the dipolarization flow, as suggested by our modeling results.

Computer simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces.

A prominent feature of coronaviruses is the presence of a large glycoprotein spike protruding from a lipidic membrane. This glycoprotein spike determines the interaction of coronaviruses with the environment and the host. In this paper, we perform all atomic molecular dynamics simulations of the interaction between the SARS-CoV-2 trimeric glycoprotein spike and surfaces of materials. We considered a material with high hydrogen bonding capacity (cellulose) and a material capable of strong hydrophobic interactions (graphite). Initially, the spike adsorbs to both surfaces through essentially the same residues belonging to the receptor binding subunit of its three monomers. Adsorption onto cellulose stabilizes in this configuration, with the help of a large number of hydrogen bonds developed between cellulose and the three receptor-binding domains of the glycoprotein spike. In the case of adsorption onto graphite, the initial adsorption configuration is not stable and the surface induces a substantial deformation of the glycoprotein spike with a large number of adsorbed residues not pertaining to the binding subunits of the spike monomers.

Constraining Ion-Scale Heating and Spectral Energy Transfer in Observations of Plasma Turbulence.

We perform a statistical study of the turbulent power spectrum at inertial and kinetic scales observed during the first perihelion encounter of the Parker Solar Probe. We find that often there is an extremely steep scaling range of the power spectrum just above the ion-kinetic scales, similar to prior observations at 1 A.U., with a power-law index of around -4. Based on our measurements, we demonstrate that either a significant (>50%) fraction of the total turbulent energy flux is dissipated in this range of scales, or the characteristic nonlinear interaction time of the turbulence decreases dramatically from the expectation based solely on the dispersive nature of nonlinearly interacting kinetic Alfvén waves.

Atomistic Simulations of COSAN: Amphiphiles without a Head-and-Tail Design Display "Head and Tail" Surfactant Behavior.

Cobaltabisdicarbollide (COSAN) anions have an unexpectedly rich self-assembly behavior, which can lead to vesicles and micelles without having a classical surfactant molecular architecture. This was rationalized by the introduction of new terminology and novel driving forces. A key aspect in the interpretation of COSAN behavior is the assumption that the most stable form of these ions is the transoid rotamer, which lacks a "hydrophilic head" and a "hydrophobic tail". Using implicit solvent DFT calculations and MD simulations we show that in water, 1) the cisoid rotamer is the most stable form of COSAN and 2) this cisoid rotamer has a well-defined hydrophilic polar region ("head") and a hydrophobic apolar region ("tail"). In addition, our simulations show that the properties of this rotamer in water (interfacial affinity, micellization) match those expected for a classical surfactant. Therefore, we conclude that the experimental results for the COSAN ions can now be understood in terms of its amphiphilic molecular architecture.

Surface specificity and mechanistic pathway of de-fluorination of C60F48 on coinage metals.

We provide experimental and theoretical understanding on fundamental processes taking place at room temperature when a fluorinated fullerene dopant gets close to a metal surface. By employing scanning tunneling microscopy and photoelectron spectroscopies, we demonstrate that the on-surface integrity of C60F48 depends on the interaction with the particular metal it approaches. Whereas on Au(111) the molecule preserves its chemical structure, on more reactive surfaces such as Cu(111) and Ni(111), molecules interacting with the bare metal surface lose the halogen atoms and transform to C60. Though fluorine-metal bonding can be detected depending on the molecular surface density, no ordered fluorine structures are observed. We show the implications of the metal-dependent de-fluorination in the electronic structure of the molecules and the energy alignment at the molecule-metal interface. Molecular dynamics simulations with ReaxFF reactive force field corroborate the experimental facts and provide a detailed mechanistic picture of the surface-induced de-fluorination, which involves the rotation of the molecule on the surface. Outstandingly, a thermodynamic analysis indicates that the effect of the metal surface is lowering and diminishing the energy barrier for C-F cleave, demonstrating the catalytic role of the surface. The present study contributes to in-depth knowledge of the mechanisms that affect the degree of stability of chemical species on surfaces, which is essential to advance our understanding of the chemical reactivity of metals and their role in on-surface chemical reactions.

Effect of collagenase-gelatinase ratio on the mechanical properties of a collagen fibril: a combined Monte Carlo-molecular dynamics study.

Loading in cartilage is supported primarily by fibrillar collagen, and damage will impair the function of the tissue, leading to pathologies such as osteoarthritis. Damage is initiated by two types of matrix metalloproteinases, collagenase and gelatinase, that cleave and denature the collagen fibrils in the tissue. Experimental and modeling studies have revealed insights into the individual contributions of these two types of MMPs, as well as the mechanical response of intact fibrils and fibrils that have experienced random surface degradation. However, no research has comprehensively examined the combined influences of collagenases and gelatinases on collagen degradation nor studied the mechanical consequences of biological degradation of collagen fibrils. Such preclinical examinations are required to gain insights into understanding, treating, and preventing degradation-related cartilage pathology. To develop these insights, we use sequential Monte Carlo and molecular dynamics simulations to probe the effect of enzymatic degradation on the structure and mechanics of a single collagen fibril. We find that the mechanical response depends on the ratio of collagenase to gelatinase-not just the amount of lost fibril mass-and we provide a possible mechanism underlying this phenomenon. Overall, by characterizing the combined influences of collagenases and gelatinases on fibril degradation and mechanics at the preclinical research stage, we gain insights that may facilitate the development of targeted interventions to prevent the damage and loss of mechanical integrity that can lead to cartilage pathology.

Molecular insight into the wetting behavior and amphiphilic character of cellulose nanocrystals.

The study of nanocellulose is a field of growing interest due to its many applications and its use in the development of biocompatible and eco-friendly materials. In spite of the vast number of studies in the field, many questions about the role of the molecular structure in the properties of cellulose are still subject of debate. One of these fundamental questions is the possible amphiphilic nature of cellulose and the relative role of hydrogen bonding and hydrophobic effect on the interactions of cellulose. In this work we present an extensive molecular dynamics simulation study of this question by analyzing the wetting of cellulose with water and organic solvent, its interaction with hydrophilic and hydrophobic ions and its interaction with a protein (human epidermal growth factor, hEGF). We consider two characteristic cellulose crystal planes of Iß cellulose with very different roughness, different hydrogen bonding capability and different exposure of cellulose hydrophobic groups (the (010) plane which has exposed -OH groups and the (100) plane with buried -OH groups). Our results show that both surfaces are simultaneously hydrophilic and lipophilic, with both surfaces having very similar contact angles. In spite of the global similarity of wetting of both surfaces, the molecular details of wetting are very different and substantial local wetting heterogeneities (which strongly depend on the surface) appear for both solvents. We also observe a weak interaction of both surfaces with hydrophobic and hydrophilic solutes. These weak interactions are attributed to the simultaneous lipophilic and hydrophilic character of both (100) and (010) cellulose surfaces. Interestingly, we found a substantial interaction of both cellulose planes with polar and apolar residues of the hEGF protein.

Insights into Preformed Human Serum Albumin Corona on Iron Oxide Nanoparticles: Structure, Effect of Particle Size, Impact on MRI Efficiency, and Metabolization.

In the past decade, profuse research efforts explored the uses of iron oxide particles in nanomedicine. To a great extent, the efficiency and fate of those magnetic nanoparticles depend on how their surfaces interface with the proteins in a physiological environment. It is well reported how an ungoverned protein corona can be detrimental to cellular uptake and targeting efficiency and how it can modify the nanoparticles biodistribution. Novel strategies are emerging to achieve enhanced and more reproducible performances of engineered nanoparticles with a custom-built protein corona. Here we report on a generalized protocol to preform a monolayer of human serum albumin (HSA) on superparamagnetic iron oxide nanoparticles (SPIONs) of different sizes. The resulting molecular structures are described by molecular dynamics simulations of the hybrid nanoconjugates. The simulations outcomes regarding the number of proteins in the corona and their monolayer arrangement on the particle surface are in agreement with the results obtained from dynamic light scattering and electronic microscopy analysis. Using tryptophan fluorescence quenching, we revealed the existence of a strong interaction between the SPIONs and the HSA which endorses the robustness of the protein-nanoparticle conjugates in this system. Moreover, we evaluated the effect of the HSA corona on the SPIONs efficiency as magnetic resonance imaging (MRI) contrast agents in water, human serum, and saline media. The protein corona did not affect the efficiency of the SPIONs as T2 contrast agents but reduce their T1 efficiency. In addition, we observed a greater stability for HSA-SPIONs nanoconjugates in saline and in acid media, preventing nanoparticle dissolution in extreme gastric conditions.

Kinetic Equilibrium of Dipolarization Fronts.

The unprecedented high-resolution data from the Magnetospheric Multi-Scale (MMS) satellites is revealing the physics of dipolarization fronts created in the aftermath of magnetic reconnection in extraordinary detail. The data shows that the fronts contain structures on small spatial scales beyond the scope of fluid framework. A new kinetic analysis, applied to MMS data here, predicts that global plasma compression produces a unique particle distribution in a narrow boundary layer with separation of electron and ion scale physics. Layer widths on the order of an ion gyro-diameter lead to an ambipolar potential across the magnetic field resulting in strongly sheared flows. Gradients along the magnetic field lines create a potential difference, which can accelerate ions and electrons into beams. These small-scale kinetic effects determine the plasma dynamics in dipolarization fronts, including the origin of the distinctive broadband emissions.

Coarse-grained molecular dynamics simulation of the interface behaviour and self-assembly of CTAB cationic surfactants.

In this work we study the behaviour at interfaces and the micelle self-assembly of a cationic surfactant (CTAB) by Molecular Dynamics (MD) simulations of coarse-grained models. We consider both the standard (with explicit water) Martini force field and the implicit solvent version of the Martini force field (Dry Martini). First, we study the behaviour of CTAB at a water/vacuum interface, at a water/organic solvent interface and in a pre-assembled CTAB micelle using both standard and Dry Martini and all-atomic simulations. Our results indicate that there are significant quantitative differences between the predictions of the two models. Interestingly, implicit solvent simulations with Dry Martini show good quantitative agreement with all-atomic MD simulations, better than explicit solvent Martini MD simulations. The computational efficiency of the Martini and Dry Martini models allowed us to study the self-assembly of CTAB in a large system with many micelles. We observe the self-assembly of CTAB into micelles and also the exchange of CTAB molecules between micelles by events such as micelle fusion and fission which are difficult to observe in all-atomic MD simulations due to the time and length scales involved. Under the studied conditions, both Martini models predict a rather different self-assembly behaviour. The standard Martini model predicts a final equilibrium state with spherical micelles with an average size of ≈70 CTAB molecules. In contrast, the Dry Martini model predicts the formation of large tubular micelles with ≈330 CTAB molecules. Compared with experiments, standard Martini and Dry Martini underestimate and overestimate, respectively, the micelle size.

Studies on electrostatic interactions within model nano-confined aqueous environments of different chemical nature.

We study the potential of mean force for pairs of parallel flat surfaces with attractive electrostatic interactions by employing model systems functionalized with different charged, hydrophobic and hydrophilic groups. We study the way in which the local environment (hydrophobic or hydrophilic moieties) modulates the interaction between the attractive charged groups on the plates by removing or attracting nearby water and thus screening or not the electrostatic interaction. To explicitly account for the role of the solvent and the local hydrophobicity, we also perform studies in vacuo. Additionally, the results are compared to that for non-charged plates in order to single out and rationalize the non-additivity of the different non-covalent interactions. Our simulations demonstrate that the presence of neighboring hydrophobic groups promote water removal in the vicinity of the charged groups, thus enhancing charge attraction upon self-assembly. This role of the local hydrophobicity modulating electrostatic interactions is consistent with recent qualitative descriptions in the protein binding context.

Behavior of ligand binding assays with crowded surfaces: Molecular model of antigen capture by antibody-conjugated nanoparticles.

Ligand-receptor binding is of utmost importance in several biologically related disciplines. Ligand binding assays (LBA) use the high specificity and high affinity of ligands to detect, target or measure a specific receptors. One particular example of ligand binding assays are Antibody conjugated Nanoparticles (AcNPs), edge-cutting technologies that are present in several novel biomedical approaches for imaging, detection and treatment of diseases. However, the nano-confinement in AcNPs and LBA nanostructures introduces extra complexity in the analysis of ligand-receptor equilibriums. Because antibodies are large voluminous ligands, the effective affinity in AcNPs is often determined by antibody orientation and surface coverage. Moreover, antibodies have two binding sites introducing an extra ligand-receptor binding equilibrium. As consequence of all this, experimental or theoretical studies providing a guidelines for the prediction of the binding behavior in AcNPs are scarce. In this work, we present a set of theoretical calculations to shed light into the complex binding behavior of AcNPs and its implications in biomedical applications. To investigate the ligand-receptor binding on AcNPs, we have used a molecular theory that predicts the probability of different molecular conformations of the system depending on the local environment. We have considered two different pathways for designing these devices: covalently conjugated antibodies and streptavidin-biotin conjugated antibodies. We also explore the effects of surface coverage, bulk concentrations, nanoparticle size and antibody-antigen affinity. Overall, this work offers a series of theoretical predictions that can be used as a guide in the design of antibody conjugated nanoparticles for different applications.

Mechanical properties of a collagen fibril under simulated degradation.

Collagen fibrils are a very important component in most of the connective tissue in humans. An important process associated with several physiological and pathological states is the degradation of collagen. Collagen degradation is usually mediated by enzymatic and non-enzymatic processes. In this work we use molecular dynamics simulations to study the influence of simulated degradation on the mechanical properties of the collagen fibril. We applied tensile stress to the collagen fiber at different stages of degradation. We compared the difference in the fibril mechanical priorities due the removal of enzymatic crosslink, surface degradation and volumetric degradation. As anticipated, our results indicated that, regardless of the degradation scenario, fibril mechanical properties is reduced. The type of degradation mechanism (crosslink, surface or volumetric) expressed differential effect on the change in the fibril stiffness. Our simulation results showed dramatic change in the fibril stiffness with a small amount of degradation. This suggests that the hierarchical structure of the fibril is a key component for the toughness and is very sensitive to changes in the organization of the fibril. The overall results are intended to provide a theoretical framework for the understanding the mechanical behavior of collagen fibrils under degradation.

Structure and dynamics of high- and low-density water molecules in the liquid and supercooled regimes.

By combining the local structure index with potential energy minimisations we study the local environment of the water molecules for a couple of water models, TIP5P-Ew and SPC/E, in order to characterise low- and high-density "species". Both models show a similar behaviour within the supercooled regime, with two clearly distinguishable populations of unstructured and structured molecules, the fraction of the latter increasing with supercooling. Additionally, for TIP5P-Ew, we find that the structured component vanishes quickly at the normal liquid regime (above the melting temperature). Thus, while SPC/E provides a fraction of structured molecules similar to that found in X-ray experiments, we show that TIP5P-Ew underestimates such value. Moreover, unlike SPC/E, we demonstrate that TIP5P-Ew does not follow the linear dependence of the logarithm of the structured fraction with inverse temperature, as predicted by the two-order parameter model. Finally, we link structure to dynamics by showing that there exists a strong correlation between structural fluctuation and dynamics in the supercooled state with spatial correlations in both static and dynamic quantities.

Selective Depletion of αß T Cells and B Cells for Human Leukocyte Antigen-Haploidentical Hematopoietic Stem Cell Transplantation. A Three-Year Follow-Up of Procedure Efficiency.

HLA-haploidentical family donors represent a valuable option for children requiring allogeneic hematopoietic stem cell transplantation (HSCT). Because graft-versus-host diseases (GVHD) is a major complication of HLA-haploidentical HSCT because of alloreactive T cells in the graft, different methods have been used for ex vivo T cell depletion. Removal of donor αß T cells, the subset responsible for GVHD, and of B cells, responsible for post-transplantation lymphoproliferative disorders, have been recently developed for HLA-haploidentical HSCT. This manipulation preserves, in addition to CD34+ progenitors, natural killer, γδ T, and monocytes/dendritic cells, contributing to anti-leukemia activity and protection against infections. We analyzed depletion efficiency and cell yield in 200 procedures performed in the last 3 years at our center. Donors underwent CD34+ hematopoietic stem cell (HSC) peripheral blood mobilization with granulocyte colony-stimulating factor (G-CSF). Poor CD34+ cell mobilizers (48 of 189, 25%) received plerixafor in addition to G-CSF. Aphereses containing a median of 52.5 × 109 nucleated cells and 494 × 106 CD34+ HSC were manipulated using the CliniMACS device. In comparison to the initial product, αß T cell depletion produced a median 4.1-log reduction (range, 3.1 to 5.5) and B cell depletion led to a median 3.4-log reduction (range, 2.0 to 4.7). Graft products contained a median of 18.5 × 106 CD34+ HSC/kg recipient body weight, with median values of residual αß T cells and B cells of 29 × 103/kg and 33 × 103/kg, respectively. Depletion efficiency monitored at 6-month intervals demonstrated steady performance, while improved recovery of CD34+ cells was observed after the first year (P = .0005). These data indicate that αß T cell and B cell depletion of HSC grafts from HLA-haploidentical donors was efficient and reproducible.

Enhanced binding of antibodies generated during chronic HIV infection to mucus component MUC16.

Transmission of HIV across mucosal barriers accounts for the majority of HIV infections worldwide. Thus, efforts aimed at enhancing protective immunity at these sites are a top priority, including increasing virus-specific antibodies (Abs) and antiviral activity at mucosal sites. Mucin proteins, including the largest cell-associated mucin, mucin 16 (MUC16), help form mucus to provide a physical barrier to incoming pathogens. Here, we describe a natural interaction between Abs and MUC16 that is enhanced in specific disease settings such as chronic HIV infection. Binding to MUC16 was independent of IgG subclass, but strongly associated with shorter Ab glycan profiles, with agalactosylated (G0) Abs demonstrating the highest binding to MUC16. Binding of Abs to epithelial cells was diminished following MUC16 knockdown, and the MUC16 N-linked glycans were critical for binding. Further, agalactosylated VRC01 captured HIV more efficiently in MUC16. These data point to a novel opportunity to enrich Abs at mucosal sites by targeting Abs to MUC16 through changes in Fc glycosylation, potentially blocking viral movement and sequestering the virus far from the epithelial border. Thus, next-generation vaccines or monoclonal therapeutics may enhance protective immunity by tuning Ab glycosylation to promote the enrichment of Abs at mucosal barriers.

Controlling the hydration rate of a hydrophilic matrix in the core of an intravaginal ring determines antiretroviral release.

Intravaginal ring technology is generally limited to releasing low molecular weight species that can diffuse through the ring elastomer. To increase the diversity of drugs that can be delivered from intravaginal rings, we designed an IVR that contains a drug matrix encapsulated in the core of the IVR whereby the mechanism of drug release is uncoupled from the interaction of the drug with the ring elastomer. We call the device a flux controlled pump, and it is comprised of compressed pellets of a mixture of drug and hydroxypropyl cellulose within the hollow core of the ring. The pump orifice size and chemistry of the polymer pellets control the rate of hydration and diffusion of the drug-containing hydroxypropyl cellulose gel from the device. A mechanistic model describing the hydration and diffusion of the hydroxypropyl cellulose matrix is presented. Good agreement between the quantitative model predictions and the experimental studies of drug release was obtained. We achieved controlled release rates of multiple antiretrovirals ranging from µg/d to mg/d by altering the orifice design, drug loading, and mass of pellets loaded in the device. This device could provide an adaptable platform for the vaginal drug delivery of many molecules.