dtool and dserver: A flexible ecosystem for findable data.

Making data FAIR-findable, accessible, interoperable, reproducible-has become the recurring theme behind many research data management efforts. dtool is a lightweight data management tool that packages metadata with immutable data to promote accessibility, interoperability, and reproducibility. Each dataset is self-contained and does not require metadata to be stored in a centralised system. This decentralised approach means that finding datasets can be difficult. dtool's lookup server, short dserver, as defined by a REST API, makes dtool datasets findable, hence rendering the dtool ecosystem fit for a FAIR data management world. Its simplicity, modularity, accessibility and standardisation via API distinguish dtool and dserver from other solutions and enable it to serve as a common denominator for cross-disciplinary research data management. The dtool ecosystem bridges the gap between standardisation-free data management by individuals and FAIR platform solutions with rigid metadata requirements.

O-glycans Expand Lubricin and Attenuate Its Viscosity and Shear Thinning.

Lubricin, an intrinsically disordered glycoprotein, plays a pivotal role in facilitating smooth movement and ensuring the enduring functionality of synovial joints. The central domain of this protein serves as a source of this excellent lubrication and is characterized by its highly glycosylated, negatively charged, and disordered structure. However, the influence of O-glycans on the viscosity of lubricin remains unclear. In this study, we employ molecular dynamics simulations in the absence and presence of shear, along with continuum simulations, to elucidate the intricate interplay between O-glycans and lubricin and the impact of O-glycans on lubricin's conformational properties and viscosity. We found the presence of O-glycans to induce a more extended conformation in fragments of the disordered region of lubricin. These O-glycans contribute to a reduction in solution viscosity but at the same time weaken shear thinning at high shear rates, compared to nonglycosylated systems with the same density. This effect is attributed to the steric and electrostatic repulsion between the fragments, which prevents their conglomeration and structuring. Our computational study yields a mechanistic mechanism underlying previous experimental observations of lubricin and paves the way to a more rational understanding of its function in the synovial fluid.

Why soft contacts are stickier when breaking than when making them.

Soft solids are sticky. They attract each other and spontaneously form a large area of contact. Their force of attraction is higher when separating than when forming contact, a phenomenon known as adhesion hysteresis. The common explanation for this hysteresis is viscoelastic energy dissipation or contact aging. Here, we use experiments and simulations to show that it emerges even for perfectly elastic solids. Pinning by surface roughness triggers the stick-slip motion of the contact line, dissipating energy. We derive a simple and general parameter-free equation that quantitatively describes contact formation in the presence of roughness. Our results highlight the crucial role of surface roughness and present a fundamental shift in our understanding of soft adhesion.

The bumpy road to friction control.

The frictional properties of material interfaces can be rationally designed.

Toward a continuum description of lubrication in highly pressurized nanometer-wide constrictions: The importance of accurate slip laws.

The Reynolds lubrication equation (RLE) is widely used to design sliding contacts in mechanical machinery. While providing an excellent description of hydrodynamic lubrication, friction in boundary lubrication regions is usually considered by empirical laws, because continuum theories are expected to fail for lubricant film heights h0 ≪ 10 nm, especially in highly loaded tribosystems with normal pressures pn ≫ 0.1 GPa. Here, the performance of RLEs is validated by molecular dynamics simulations of pressurized (with pn = 0.2 to 1 GPa) hexadecane in a gold converging-diverging channel with minimum gap heights h0 = 1.4 to 9.7 nm. For pn ≤ 0.4 GPa and h0 ≥ 5 nm, agreement with the RLE requires accurate constitutive laws for pressure-dependent density and viscosity. An additional nonlinear wall slip law relating wall slip velocities to local shear stresses extends the RLE's validity to even the most severe loading condition pn = 1 GPa and h0 = 1.4 nm. Our results demonstrate an innovative route for continuum modeling of highly loaded tribological contacts under boundary lubrication.

Confinement-Induced Diffusive Sound Transport in Nanoscale Fluidic Channels.

Molecular dynamics (MD) simulations have been widely used to study flow at molecular scales. Most of this work is devoted to study the departure from continuum fluid mechanics as the confining dimension decreases. Here, we present MD results under conditions where hydrodynamic descriptions typically apply, but focus on the influence of in-plane wavelengths. Probing the long wavelength limit in thermodynamic equilibrium, we observed anomalous relaxation of the density and longitudinal momentum fluctuations. The limiting behavior can be described by an effective continuum theory that describes a transition to overdamped sound relaxation for compressible fluids.

Entropic stress of grafted polymer chains in shear flow.

We analyze the shear response of grafted polymer chains in shear flow via coarse-grained molecular dynamics simulations with an explicit solvent. We find that the solvent flow penetrates into almost the whole brush for "mushroom"-type brushes but only a few bond distances for dense brushes. In all cases, the external stress on the wall equals the entropic stress associated with the distorted polymer conformations. We find that the external stress increases linearly with shear rate at low rates and sublinearly at high rates. The transition from linear to sublinear scaling occurs where chains react to flow by reorienting. Sublinear scaling with shear rate disappears if the shear rate is nondimensionalized with the effective relaxation time of chain subsegments located in the outer part of the brush that experiences flow.

Molecular simulations of sliding on SDS surfactant films.

We use molecular dynamics simulations to study the frictional response of monolayers of the anionic surfactant sodium dodecyl sulfate and hemicylindrical aggregates physisorbed on gold. Our simulations of a sliding spherical asperity reveal the following two friction regimes: at low loads, the films show Amonton's friction with a friction force that rises linearly with normal load, and at high loads, the friction force is independent of the load as long as no direct solid-solid contact occurs. The transition between these two regimes happens when a single molecular layer is confined in the gap between the sliding bodies. The friction force at high loads on a monolayer rises monotonically with film density and drops slightly with the transition to hemicylindrical aggregates. This monotonous increase of friction force is compatible with a traditional plowing model of sliding friction. At low loads, the friction coefficient reaches a minimum at the intermediate surface concentrations. We attribute this behavior to a competition between adhesive forces, repulsion of the compressed film, and the onset of plowing.

Elastic property and fracture mechanics of lateral branch-branch junctions in cacti: A case study of Opuntia ficus-indica and Cylindropuntia bigelovii.

Species with various reproductive modes accompanied by different mechanical properties of their (lateral) branch-branch junctions have evolved in the cactus subfamily Opuntioideae. Older branches of Opuntia ficus-indica with fracture-resistant junctions often bear flowers and fruits for sexual reproduction, whereas younger branches break off easily and provide offshoots for vegetative propagation. Cylindropuntia bigelovii plants are known for their vegetative reproduction via easily detachable branches that can establish themselves as offshoots. We characterized the elastic and fracture behaviors of these lateral junctions by tensile testing and analyzed local strains during loading. Additionally, we carried out finite element analyses to quantify the influence of five relevant tissue layers on joint elastic behavior. Our fracture analysis revealed various fracture modes: (i) most young samples of Opuntia ficus-indica failed directly at the junction and had smooth fracture surfaces, and relative fracture strain was on median 4% of the total strain; (ii) most older samples of Opuntia ficus-indica failed at the adjacent branch and exhibited rough fracture surfaces, and relative fracture strain was on median 47%; (iii) most samples of Cylindropuntia bigelovii abscised directly at the junction and exhibited cup and cone surfaces, and relative fracture strain was on median 28%. Various geometric and mechanical properties such as junction area, fracture energy, and tensile strength were analyzed with respect to significant differences between species and age of sample. Interestingly, the abscission of lateral branches naturally triggered by wind, passing animals, or vibration showed the following differences in maximum force: 153 N (older Opuntia ficus-indica), 51 N (young Opuntia ficus-indica), and 14 N (Cylindropuntia bigelovii).

Dependence of adhesive friction on surface roughness and elastic modulus.

Friction is one of the leading causes of energy loss in moving parts, and understanding how roughness affects friction is of utmost importance. From creating surfaces with high friction to prevent slip and movement, to creating surfaces with low friction to minimize energy loss, roughness plays a key role. By measuring shear stresses of crosslinked elastomers on three rough surfaces of similar surface chemistry across nearly six decades of sliding velocity, we demonstrate the dominant role of adhesive frictional dissipation. Furthermore, while it was previously known that roughness-induced oscillations affected the viscoelastic dissipation, we show that these oscillations also control the molecular detachment process and the resulting adhesive dissipation. This contrasts with typical models of friction, where only the amount of contact area and the strength of interfacial bonding govern the adhesive dissipation. Finally, we show that all the data can be collapsed onto a universal curve when the shear stress is scaled by the square root of elastic modulus and the velocity is scaled by a critical velocity at which the system exhibits macroscopic buckling instabilities. Taken together, these results suggest a design principle broadly applicable to frictional systems ranging from tires to soft robotics.

Surface topography as a material parameter.

Abstract: Materials science is about understanding the relationship between a material's structure and its properties-in the sphere of mechanical behavior, this includes elastic modulus, yield strength, and other bulk properties. We show in this issue that, analogously, a material's surface structure governs its surface properties-such as adhesion, friction, and surface stiffness. For bulk materials, microstructure is a critical component of structure; for surfaces, the structure is governed largely by surface topography. The articles in this issue cover the latest understanding of these structure-property connections for surfaces. This includes both the theoretical basis for how properties depend on topography, as well as the latest understanding of how surface topography emerges, how to measure and understand topography-dependent properties, and how to engineer surfaces to improve performance. The present article frames the importance of surface topography and its effect on properties; it also outlines some of the critical knowledge gaps that impede progress toward optimally performing surfaces.

Solid-Phase Silicon Homoepitaxy via Shear-Induced Amorphization and Recrystallization.

We study mechanically induced phase transitions at tribological interfaces between silicon crystals using reactive molecular dynamics. The simulations reveal that the interplay between shear-driven amorphization and recrystallization results in an amorphous shear interface with constant thickness. Different shear elastic responses of the two anisotropic crystals can lead to the migration of the amorphous interface normal to the sliding plane, causing the crystal with lowest elastic energy density to grow at the expense of the other one. This triboepitaxial growth can be achieved by crystal misorientation or exploiting elastic finite-size effects, enabling the direct deposition of homoepitaxial silicon nanofilms by a crystalline tip rubbing against a substrate.

Green's function method for dynamic contact calculations.

Resolving atomic scale details while capturing long-range elastic deformation is the principal difficulty when solving contact mechanics problems with computer simulations. Fully atomistic simulations must consider large blocks of atoms to support long-wavelength deformation modes, meaning that most atoms are far removed from the region of interest. Building on earlier methods that used elastic surface Green's functions to compute static substrate deformation, we present a numerically efficient dynamic Green's function technique to treat realistic, time-evolving, elastic solids. Our method solves substrate dynamics in reciprocal space and utilizes precomputed Green's functions that exactly reproduce elastic interactions without retaining the atomic degrees of freedom in the bulk. We invoke physical insights to determine the necessary number of explicit substrate layers required to capture the attenuation of subsurface waves as a function of surface wave vector. We observe that truncating substrate dynamics at depths that fall as a power of wave vector allows us to accurately model wave propagation without implementing arbitrary damping. The framework we have developed substantially accelerates molecular dynamics simulations of large elastic substrates. We apply the method to single asperity contact, impact, and sliding friction problems and present our preliminary findings.

The emergence of small-scale self-affine surface roughness from deformation.

Most natural and man-made surfaces appear to be rough on many length scales. There is presently no unifying theory of the origin of roughness or the self-affine nature of surface topography. One likely contributor to the formation of roughness is deformation, which underlies many processes that shape surfaces such as machining, fracture, and wear. Using molecular dynamics, we simulate the biaxial compression of single-crystal Au, the high-entropy alloy Ni36.67Co30Fe16.67Ti16.67, and amorphous Cu50Zr50 and show that even surfaces of homogeneous materials develop a self-affine structure. By characterizing subsurface deformation, we connect the self-affinity of the surface to the spatial correlation of deformation events occurring within the bulk and present scaling relations for the evolution of roughness with strain. These results open routes toward interpreting and engineering roughness profiles.

Linking energy loss in soft adhesion to surface roughness.

A mechanistic understanding of adhesion in soft materials is critical in the fields of transportation (tires, gaskets, and seals), biomaterials, microcontact printing, and soft robotics. Measurements have long demonstrated that the apparent work of adhesion coming into contact is consistently lower than the intrinsic work of adhesion for the materials, and that there is adhesion hysteresis during separation, commonly explained by viscoelastic dissipation. Still lacking is a quantitative experimentally validated link between adhesion and measured topography. Here, we used in situ measurements of contact size to investigate the adhesion behavior of soft elastic polydimethylsiloxane hemispheres (modulus ranging from 0.7 to 10 MPa) on 4 different polycrystalline diamond substrates with topography characterized across 8 orders of magnitude, including down to the angstrom scale. The results show that the reduction in apparent work of adhesion is equal to the energy required to achieve conformal contact. Further, the energy loss during contact and removal is equal to the product of the intrinsic work of adhesion and the true contact area. These findings provide a simple mechanism to quantitatively link the widely observed adhesion hysteresis to roughness rather than viscoelastic dissipation.

Chemical aging of large-scale randomly rough frictional contacts.

It has been shown that contact aging due to chemical reactions in single asperity contacts can have a significant effect on friction. However, it is currently unknown how chemically induced contact aging of friction depends on roughness that is typically encountered in macroscopic rough contacts. Here we develop an approach that brings together a kinetic Monte Carlo model of chemical aging with a contact mechanics model of rough surfaces based on the boundary element method to determine the magnitude of chemical aging in silica-silica contacts with random roughness. Our multiscale model predicts that chemical aging for randomly rough contacts has a logarithmic dependence on time. It also shows that friction aging switches from a linear to a nonlinear dependence on the applied load as the load increase. We discover that surface roughness affects the aging behavior primarily by modifying the real contact area and the local contact pressure, whereas the effect of contact morphology is relatively small. Our results demonstrate how understanding of chemical aging can be translated from studies of single asperity contacts to macroscopic rough contacts.

Combining TEM, AFM, and Profilometry for Quantitative Topography Characterization Across All Scales.

Surface roughness affects the functional properties of surfaces, including adhesion, friction, hydrophobicity, biological response, and electrical and thermal transport properties. However, experimental investigations to quantify these links are often inconclusive because surfaces are fractal-like, and the values of measured roughness parameters depend on measurement size. Here, we demonstrate the characterization of topography of an ultrananocrystalline diamond (UNCD) surface at the angstrom scale using transmission electron microscopy (TEM), as well as its combination with conventional techniques to achieve a comprehensive surface description spanning 8 orders of magnitude in size. We performed more than 100 individual measurements of the nanodiamond film using both TEM and conventional techniques (stylus profilometry and atomic force microscopy). While individual measurements of root-mean-square (RMS) height, RMS slope, and RMS curvature vary by orders of magnitude, we combine the various techniques using the power spectral density and use this to compute scale-independent parameters. This analysis reveals that "smooth" UNCD surfaces have an RMS slope greater than 1, even larger than the slope of the Austrian Alps when measured on the scale of a human step. This approach of comprehensive multiscale roughness characterization, measured with angstrom-scale detail, will enable the systematic evaluation and optimization of other technologically relevant surfaces, as well as systematic testing of the many analytical and numerical models for the behavior of rough surfaces.

The atomic simulation environment-a Python library for working with atoms.

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Molecular Dynamic Simulation of Collision-Induced Third-Body Formation in Hydrogen-Free Diamond-Like Carbon Asperities.

The collision of two cylindrical hydrogen-free diamond-like carbon (DLC) asperities with approximately 60 % sp3 hybridization has been studied using classical molecular dynamics. The severity of the collision can be controlled by the impact parameter b that measures the width of the projected overlap of the two cylinders. For a cylinder radius of R = 23 nm, three collisions with b = 0.5 nm, b = 1 nm and b = 2.0 nm are compared. While for the two small b a single shear band between the collision partners and a strongly localized sp2/sp1 hybridised third-body zone between the asperities is observed, the b = 2 nm collision is accompanied by pronounced plastic deformation in both asperities that destabilize the metastable sp3-rich phase leading to a drastic increase in the amount of rehybridized tribomaterial. In addition, pronounced roughening of the cylinder surfaces, asymmetric material transfer and the generation of wear debris are found in this case. For the b = 0.5 and 1 nm collision, the evolution of third-body volume can be quantitatively described by a simple geometric overlap model that assumes a sliding-induced phase transformation localized between both asperities. For b = 2 nm, this model underestimates the third-body volume by more than 150 % indicating that plasticity has to be taken into account in simple geometric models of severe DLC/DLC asperity collisions.

Boundary lubrication of heterogeneous surfaces and the onset of cavitation in frictional contacts.

Surfaces can be slippery or sticky depending on surface chemistry and roughness. We demonstrate in atomistic simulations that regular and random slip patterns on a surface lead to pressure excursions within a lubricated contact that increase quadratically with decreasing contact separation. This is captured well by a simple hydrodynamic model including wall slip. We predict with this model that pressure changes for larger length scales and realistic frictional conditions can easily reach cavitation thresholds and significantly change the load-bearing capacity of a contact. Cavitation may therefore be the norm, not the exception, under boundary lubrication conditions.