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.

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.

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.

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.

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.

Near-Earth injection of MeV electrons associated with intense dipolarization electric fields: Van Allen Probes observations.

Substorms generally inject tens to hundreds of keV electrons, but intense substorm electric fields have been shown to inject MeV electrons as well. An intriguing question is whether such MeVelectron injections can populate the outer radiation belt. Here we present observations of a substorm injection of MeV electrons into the inner magnetosphere. In the premidnight sector at L ∼ 5.5, Van Allen Probes (Radiation Belt Storm Probes)-A observed a large dipolarization electric field (50 mV/m) over ∼40 s and a dispersionless injection of electrons up to ∼3 MeV. Pitch angle observations indicated betatron acceleration of MeV electrons at the dipolarization front. Corresponding signals of MeV electron injection were observed at LANL-GEO, THEMIS-D, and GOES at geosynchronous altitude. Through a series of dipolarizations, the injections increased the MeV electron phase space density by 1 order of magnitude in less than 3 h in the outer radiation belt (L > 4.8). Our observations provide evidence that deep injections can supply significant MeV electrons.

Cooperative dynamic and diffusion behavior above and below the dynamical crossover of supercooled water.

Using extensive molecular dynamics simulations combined with a novel approach to analyze the molecular displacements we analyzed the change in the dynamics above and below the crossover temperature T(x) for supercooled water. Our findings suggest that the crossover from fragile to strong glass former occurring at T(x) is related with a change in the diffusion mechanism evidencing the presence of jump-like diffusion at lower temperatures. Also we observe that fluctuations of the local environments are intimately connected with fluctuations in the size and the amount of cooperative cluster of mobile molecules, and in particular we find a highly cooperative nature of the motion at low temperatures.

The water supercooled regime as described by four common water models.

The temperature scale of simple water models in general does not coincide with the natural one. Therefore, in order to make a meaningful evaluation of different water models, a temperature rescaling is necessary. In this paper, we introduce a rescaling using the melting temperature and the temperature corresponding to the maximum of the heat capacity to evaluate four common water models (TIP4P-Ew, TIP4P-2005, TIP5P-Ew and Six-Sites) in the supercooled regime. Although all the models show the same general qualitative behavior, the TIP5P-Ew appears as the best representation of the supercooled regime when the rescaled temperature is used. We also analyze, using thermodynamic arguments, the critical nucleus size for ice growth. Finally, we speculate on the possible reasons why atomistic models do not usually crystalize while the coarse grained mW model do crystallize.

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.

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.

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.

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.

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.

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.