Membrane Fluctuation Model for Understanding the Effect of Receptor Nanoclustering on the Activation of Natural Killer Cells through Biomechanical Feedback.

We investigated the role of ligand clustering and density in the activation of natural killer (NK) cells. To that end, we designed reductionist arrays of nanopatterned ligands arranged with different cluster geometries and densities and probed their effects on NK cell activation. We used these arrays as an artificial microenvironment for the stimulation of NK cells and studied the effect of the array geometry on the NK cell immune response. We found that ligand density significantly regulated NK cell activation while ligand clustering had an impact only at a specific density threshold. We also rationalized these findings by introducing a theoretical membrane fluctuation model that considers biomechanical feedback between ligand-receptor bonds and the cell membrane. These findings provide important insight into NK cell mechanobiology, which is fundamentally important and essential for designing immunotherapeutic strategies targeting cancer.

The Stokes-Einstein-Sutherland Equation at the Nanoscale Revisited.

The Stokes-Einstein-Sutherland (SES) equation is at the foundation of statistical physics, relating a particle's diffusion coefficient and size with the fluid viscosity, temperature, and the boundary condition for the particle-solvent interface. It is assumed that it relies on the separation of scales between the particle and the solvent, hence it is expected to break down for diffusive transport on the molecular scale. This assumption is however challenged by a number of experimental studies showing a remarkably small, if any, violation, while simulations systematically report the opposite. To understand these discrepancies, analytical ultracentrifugation experiments are combined with molecular simulations, both performed at unprecedented accuracies, to study the transport of buckminsterfullerene C60 in toluene at infinite dilution. This system is demonstrated to clearly violate the conditions of slow momentum relaxation. Yet, through a linear response to a constant force, the SES equation can be recovered in the long time limit with no more than 4% uncertainty both in experiments and in simulations. This nonetheless requires partial slip on the particle interface, extracted consistently from all the data. These results, thus, resolve a long-standing discussion on the validity and limits of the SES equation at the molecular scale.

Anisotropic molecular diffusion in confinement II: A model for structurally complex particles applied to transport in thin ionic liquid films.

HYPOTHESIS: Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular to interfaces, has been a standing issue and for objects of nanometric size, which structurally fluctuate on a similar time scale as they diffuse, no methodology has been established so far. We hypothesise that the complex, coupled dynamics can be captured and analysed by using a model built on the 2-dimensional Smoluchowski equation and systematic coarse-graining. METHODS AND SIMULATIONS: For large, flexible species, a universal approach is offered that does not make any assumptions about the separation of time scales between translation and other degrees of freedom. The method is validated on Molecular Dynamics simulations of bulk systems of a family of ionic liquids with increasing cation sizes where internal degrees of freedom have little to major effects. FINDINGS: After validation on bulk liquids, where we provide an interpretation of two diffusion constants for each species found experimentally, we clearly demonstrate the anisotropic nature of diffusion coefficients at interfaces. Spatial variations in the diffusivities relate to interface-induced structuring of the ionic liquids. Notably, the length scales in strongly confined ionic liquids vary consistently but differently at the solid-liquid and liquid-vapour interfaces.

Morphology as indicator of adaptive changes of model tissues in osmotically and chemically changing environments.

We investigate the formation and maintenance of the homeostatic state in the case of 2D epithelial tissues following an induction of hyperosmotic conditions, using media enriched with 80 to 320 mOsm of mannitol, NaCl, and urea. We characterise the changes in the tissue immediately after the osmotic shock, and follow it until the new homeostatic state is formed. We characterise changes in cooperative motility and proliferation pressure in the tissue upon treatment with the help of a theoretical model based on the delayed Fisher-Kolmogorov formalism, where the delay in density evolution is induced by the the finite time of the cell division. Finally we explore the adaptation of the homeostatic tissue to highly elevated osmotic conditions by evaluating the morphology and topology of cells after 20 days in incubation. We find that hyperosmotic environments together with changes in the extracellular matrix induce different mechanical states in viable tissues, where only some remain functional. The perspective is a relation between tissue topology and function, which could be explored beyond the scope of this manuscript. Experimental investigation of morphological effect of change of osmotic conditions on long-term tissue morphology and topology Effect of osmotic changes on transient tissue growth behaviour Analysis of recovery process of tissues post-osmotic-shock Toxicity limits of osmolytes in mid- to long-term tissue evolution Tissue adaptation to physiological changes in environment Long-term tissue stabilisation under altered osmotic conditions.

Block Chemistry for Accurate Modeling of Epoxy Resins.

Accurate molecular modeling of the physical and chemical behavior of highly cross-linked epoxy resins at the atomistic scale is important for the design of new property-optimized materials. However, a systematic approach to parametrizing and characterizing these systems in molecular dynamics is missing. We therefore present a unified scheme to derive atomic charges for amine-based epoxy resins, in agreement with the AMBER force field, based on defining reactive fragments─blocks─building the network. The approach is applicable to all stages of curing from pure liquid to gelation to fully cured glass. We utilize this approach to study DGEBA/DDS epoxy systems, incorporating dynamic topology changes into atomistic molecular dynamics simulations of the curing reaction with 127,000 atoms. We study size effects in our simulations and predict the gel point utilizing a rigorous percolation theory to recover accurately the experimental data. Furthermore, we observe excellent agreement between the estimated and the experimentally determined glass transition temperatures as a function of curing rate. Finally, we demonstrate the quality of our model by the prediction of the elastic modulus based on uniaxial tensile tests. The presented scheme paves the way for a broadly consistent approach for modeling and characterizing all amine-based epoxy resins.

Anisotropic molecular diffusion in confinement I: Transport of small particles in potential and density gradients.

HYPOTHESIS: Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular to interfaces, has been a standing issue. In the vicinity of interfaces, density fluctuations as a consequence of layering locally impose statistical drift, which impedes the analysis of spatially dependent diffusion coefficients even further. We hypothesise, that we can derive a model to spatially resolve interface-perpendicular diffusion coefficients based on local lifetime statistics with an extension to explicitly account for the effect of local drift using the Smoluchowski equation, that allows us to resolve anisotropic and spatially dependent diffusivity landscapes at interfaces. METHODS AND SIMULATIONS: An analytic relation between local crossing times in system slices and diffusivity as well as an explicit term for calculating drift-induced systematic errors is presented. The method is validated on Molecular Dynamics simulations of bulk water and applied to simulations of water in slit pores. FINDINGS: After validation on bulk liquids, we clearly demonstrate the anisotropic nature of diffusion coefficients at interfaces. Significant spatial variations in the diffusivities correlate with interface-induced structuring but cannot be solely attributed to the drift induced by local density fluctuations.

Demixing of homogeneous binary lipid membranes induced by protein inclusions.

We study a model of a lipid bilayer membrane described by two order parameters: the chemical composition described using the Gaussian model and the spatial configuration described with the elastic deformation model of a membrane with a finite thickness or, equivalently, for an adherent membrane. We assume and explain on physical grounds the linear coupling between the two order parameters. Using the exact solution, we calculate the correlation functions and order parameter profiles. We also study the domains that form around inclusions on the membrane. We propose and compare six distinct ways to quantify the size of such domains. Despite its simplicity, the model has many interesting features like the Fisher-Widom line and two distinct critical regions.

Observing Membrane and Cell Adhesion via Reflection Interference Contrast Microscopy.

Reflection interference contrast microscopy (RICM) is an optical microscopy technique ideally suited for imaging adhesion. While RICM (and the closely related interference reflection microscopy (IRM)) has been extensively used qualitatively or semiquantitatively to image cells, including immune cells, it can also be used quantitatively to measure membrane to surface distance, especially for model membranes. Here, we present a protocol for RICM and IRM imaging and the details of semiquantitative and quantitative analysis.

Inflammatory activation of the FcγR and IFNγR pathways co-influences the differentiation and activity of osteoclasts.

Osteoclasts are polykaryons formed by cell-cell fusion of highly motile progenitors of the myeloid lineage. Osteoclast activity can preserve skeletal strength and bone homeostasis. However, osteoclasts are responsible for bone destruction in rheumatoid arthritis (RA). Fc receptors activated by IgG immune complexes (IC) can boost osteoclast differentiation and bone loss in the course of RA. In contrast, interferon (IFN) γ secreted by immune cells blocks osteoclast activation. Despite their hypothetical importance in the regulation of osteoclast differentiation in RA, the interconnection between the two pathways has not been described so far. Here, we show by total internal reflection fluorescence (TIRF) microscopy that FcγR3 and IFNγ receptor (IFNγR) locate at close vicinity to each other on the human osteoclast surface. Moreover, the average distance increases during the differentiation process. Interestingly, FcγR and IFNγR activation shapes the position of both receptors to each other. Surprisingly, the inhibitory action of IFNγ on in-vitro human osteoclast differentiation depends on the osteoclast differentiation stage. Indeed, IFNγR activation in early osteoclast precursors completely inhibits the formation of polynucleated osteoclasts, while in premature osteoclasts, it further enhanced their fusion. In addition, gene expression analyses showed that IFNγR activation on early precursor cells but not on premature osteoclasts could induce FcγR expression, suggesting a co-regulation of both receptors on human osteoclast precursors. Phosphokinase array data of precursor cells demonstrate that the observed divergence of IFNγR signaling is dependent on the mitogen-activated protein kinase (MAPK) downstream signaling pathway. Overall, our data indicate that FcγR and IFNγR signaling pathways co-influence the differentiation and activity of osteoclasts dependent on the differentiation state, which might reflect the different stages in RA.

Improving the Performance of Supported Ionic Liquid Phase Catalysts for the Ultra-Low-Temperature Water Gas Shift Reaction Using Organic Salt Additives.

The water gas shift reaction (WGSR) is catalyzed by supported ionic liquid phase (SILP) systems containing homogeneous Ru complexes dissolved in ionic liquids (ILs). These systems work at very low temperatures, that is, between 120 and 160 °C, as compared to >200 °C in the conventional process. To improve the performance of this ultra-low-temperature catalysis, we investigated the influence of various additives on the catalytic activity of these SILP systems. In particular, the application of methylene blue (MB) as an additive doubled the activity. Infrared spectroscopy measurements combined with density functional theory (DFT) calculations excluded a coordinative interaction of MB with the Ru complex. In contrast, state-of-the-art theoretical calculations elucidated the catalytic effect of the additives by non-covalent interactions. In particular, the additives can significantly lower the barrier of the rate-determining step of the reaction mechanism via formation of hydrogen bonds. The theoretical predictions, thereby, showed excellent agreement with the increase of experimental activity upon variation of the hydrogen bonding moieties in the additives investigated.

Biomechanics as driver of aggregation of tethers in adherent membranes.

Cell adhesion is an important cellular process and is mediated by adhesion proteins residing on the cell membrane. Sometimes, two types of linker proteins are involved in adhesion, and they can segregate to form domains through a poorly understood size-exclusion process. We present an experimental and theoretical study of adhesion via linkers of two different sizes, realised in a mimetic model-system, based on giant unilamellar vesicles interacting with supported lipid bilayers. Here, adhesion is mediated by DNA linkers with two different lengths, but with the same binding enthalpy. We study the organisation of these linkers into domains as a function of relative fraction of long and short DNA constructs. Experimentally, we find that, irrespective of the composition, the adhesion domains are uniform with coexisting DNA bridge types, despite their relative difference in length of 9 nm. However, simulations suggest formation of nanodomains of the minority fraction at short length scales, which is below the optical resolution of the microscope. The nano-aggregation is more significant for long bridges, which are also more stable.

An Exact Algorithm to Detect the Percolation Transition in Molecular Dynamics Simulations of Cross-Linking Polymer Networks.

Periodic molecular dynamics simulations are developing to a routine tool for the investigation of complex, polymeric materials. A typical application is the simulation of the curing reaction of covalently cross-linked polymers, which provides detailed understanding of network formation at the molecular scale, with examples including gelation and glass transitions. In this article, we delineate the connection between percolation theory and gel-point detection in periodic polymeric networks. Specifically, we present an algorithm that can detect the onset of percolation during cross-linking of polymers in periodic molecular dynamic simulations. A sample implementation is provided at https://github.com/puls-group/percolation-analyzer. As an example, we apply the algorithm to simulations of an epoxy resin undergoing curing with an amine hardener. We also compare results with indirect gel point measurements obtained from monitoring the growth of the largest mass and the onset of secondary cycles.

Six-Color Confocal Immunofluorescence Microscopy with 4-Laser Lines.

Confocal immunofluorescence microscopy is an advanced imaging technique routinely applied in the laboratory and clinics. Histological analyses are performed from tissue material. In general, a single fluorochrome per laser is employed, limiting simultaneous analysis to four antigens in one staining with a conventional 4-laser line microscope. Here, we describe a protocol for combining fluorochromes with the same excitation but different emission properties that allows for the analysis of six different antigens in confocal immunofluorescence microscopy with a conventional 4-laser line microscope. The proposed multiplexed method permits the identification and characterization of complex cell populations in rare tissue material.

Molecular-scale spatio-chemical control of the activating-inhibitory signal integration in NK cells.

The role of juxtaposition of activating and inhibitory receptors in signal inhibition of cytotoxic lymphocytes remains strongly debated. The challenge lies in the lack of tools that allow simultaneous spatial manipulation of signaling molecules. To circumvent this, we produced a nanoengineered multifunctional platform with molecular-scale spatial control of ligands, which was applied to elucidate KIR2DL1-mediated inhibition of NKG2D signaling-receptors of natural killer cells. This platform was conceived by bimetallic nanodot patterning with molecular-scale registry, followed by a ternary functionalization with distinct moieties. We found that a 40-nm gap between activating and inhibitory ligands provided optimal inhibitory conditions. Supported by theoretical modeling, we interpret these findings as a consequence of the size mismatch and conformational flexibility of ligands in their spatial interaction. This highly versatile approach provides an important insight into the spatial mechanism of inhibitory immune checkpoints, which is essential for the rational design of future immunotherapies.

From Water Solutions to Ionic Liquids with Solid State Nanopores as a Perspective to Study Transport and Translocation Phenomena.

Solid state nanopores are single-molecular devices governed by nanoscale physics with a broad potential for technological applications. However, the control of translocation speed in these systems is still limited. Ionic liquids are molten salts which are commonly used as alternate solvents enabling the regulation of the chemical and physical interactions on solid-liquid interfaces. While their combination can be challenging to the understanding of nanoscopic processes, there has been limited attempts on bringing these two together. While summarizing the state of the art and open questions in these fields, several major advances are presented with a perspective on the next steps in the investigations of ionic-liquid filled nanopores, both from a theoretical and experimental standpoint. By analogy to aqueous solutions, it is argued that ionic liquids and nanopores can be combined to provide new nanofluidic functionalities, as well as to help resolve some of the pertinent problems in understanding transport phenomena in confined ionic liquids and providing better control of the speed of translocating analytes.

On the control of dispersion interactions between biological membranes and protein coated biointerfaces.

HYPOTHESIS: Interaction of cellular membranes with biointerfaces is of vital importance for a number of medical devices and implants. Adhesiveness of these surfaces and cells is often regulated by depositing a layer of bovine serum albumin (BSA) or other protein coatings. However, anomalously large separations between phospholipid membranes and the biointerfaces in various conditions and buffers have been observed, which could not be understood using available theoretical arguments. METHODS: Using the Lifshitz theory, we here evaluate the distance-dependent Hamaker coefficient describing the dispersion interaction between a biointerface and a membrane to understand the relative positioning of two surfaces. Our theoretical modeling is supported by experiments where the biointerface is represented by a glass substrate with deposited BSA and protein layers. These biointerfaces are allowed to interact with giant unilamellar vesicles decorated with polyethylene glycol (PEG) using PEG lipids to mimic cellular membranes and their pericellular coat. RESULTS: We demonstrate that careful treatment of the van der Waals interactions is critical for explaining the lack of adhesiveness of the membranes with protein-decorated biointerfaces. We show that BSA alone indeed passivates the glass, but depositing an additional protein layer on the surface BSA, or producing multiple layers of proteins and BSA results in repulsive dispersion forces responsible for 100 nm large equilibrium separations between the two surfaces.

Regimes of motion of magnetocapillary swimmers.

The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer's maximum velocity centred around the particle's inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations.

Molecular Biomechanics Controls Protein Mixing and Segregation in Adherent Membranes.

Cells interact with their environment by forming complex structures involving a multitude of proteins within assemblies in the plasma membrane. Despite the omnipresence of these assemblies, a number of questions about the correlations between the organisation of domains and the biomechanical properties of the involved proteins, namely their length, flexibility and affinity, as well as about the coupling to the elastic, fluctuating membrane, remain open. Here we address these issues by developing an effective Kinetic Monte Carlo simulation to model membrane adhesion. We apply this model to a typical experiment in which a cell binds to a functionalized solid supported bilayer and use two ligand-receptor pairs to study these couplings. We find that differences in affinity and length of proteins forming adhesive contacts result in several characteristic features in the calculated phase diagrams. One such feature is mixed states occurring even with proteins with length differences of 10 nm. Another feature are stable nanodomains with segregated proteins appearing on time scales of cell experiments, and for biologically relevant parameters. Furthermore, we show that macroscopic ring-like patterns can spontaneously form as a consequence of emergent protein fluxes. The capacity to form domains is captured by an order parameter that is founded on the virial coefficients for the membrane mediated interactions between bonds, which allow us to collapse all the data. These findings show that taking into account the role of the membrane allows us to recover a number of experimentally observed patterns. This is an important perspective in the context of explicit biological systems, which can now be studied in significant detail.

Maturation of Monocyte-Derived DCs Leads to Increased Cellular Stiffness, Higher Membrane Fluidity, and Changed Lipid Composition.

Dendritic cells (DCs) are professional antigen-presenting cells of the immune system. Upon sensing pathogenic material in their environment, DCs start to mature, which includes cellular processes, such as antigen uptake, processing and presentation, as well as upregulation of costimulatory molecules and cytokine secretion. During maturation, DCs detach from peripheral tissues, migrate to the nearest lymph node, and find their way into the correct position in the net of the lymph node microenvironment to meet and interact with the respective T cells. We hypothesize that the maturation of DCs is well prepared and optimized leading to processes that alter various cellular characteristics from mechanics and metabolism to membrane properties. Here, we investigated the mechanical properties of monocyte-derived dendritic cells (moDCs) using real-time deformability cytometry to measure cytoskeletal changes and found that mature moDCs were stiffer compared to immature moDCs. These cellular changes likely play an important role in the processes of cell migration and T cell activation. As lipids constitute the building blocks of the plasma membrane, which, during maturation, need to adapt to the environment for migration and DC-T cell interaction, we performed an unbiased high-throughput lipidomics screening to identify the lipidome of moDCs. These analyses revealed that the overall lipid composition was significantly changed during moDC maturation, even implying an increase of storage lipids and differences of the relative abundance of membrane lipids upon maturation. Further, metadata analyses demonstrated that lipid changes were associated with the serum low-density lipoprotein (LDL) and cholesterol levels in the blood of the donors. Finally, using lipid packing imaging we found that the membrane of mature moDCs revealed a higher fluidity compared to immature moDCs. This comprehensive and quantitative characterization of maturation associated changes in moDCs sets the stage for improving their use in clinical application.

Recent Advances and Prospects in the Research of Nascent Adhesions.

Nascent adhesions are submicron transient structures promoting the early adhesion of cells to the extracellular matrix. Nascent adhesions typically consist of several tens of integrins, and serve as platforms for the recruitment and activation of proteins to build mature focal adhesions. They are also associated with early stage signaling and the mechanoresponse. Despite their crucial role in sampling the local extracellular matrix, very little is known about the mechanism of their formation. Consequently, there is a strong scientific activity focused on elucidating the physical and biochemical foundation of their development and function. Precisely the results of this effort will be summarized in this article.