Mechanism of shaping membrane nanostructures of endoplasmic reticulum

Recent advances in super-resolution microscopy revealed the previously unknown nanoscopic level of organization of endoplasmic reticulum (ER), one of the most vital intracellular organelles. Membrane nanostructures of 10- to 100-nm intrinsic length scales, which include ER tubular matrices, ER sheet nanoholes, internal membranes of ER exit sites (ERES), and ER transport intermediates, were discovered and imaged in considerable detail, but the physical factors determining their unique geometrical features remained unknown. Here, we proposed and computationally substantiated a common concept for mechanisms of all ER nanostructures based on the membrane intrinsic curvature as a primary factor shaping the membrane and ultra-low membrane tensions as modulators of the membrane configurations. We computationally revealed a common structural motif underlying most of the nanostructures. We predicted the existence of a discrete series of equilibrium configurations of ER tubular matrices and recovered the one corresponding to the observations and favored by ultra-low tensions. We modeled the nanohole formation as resulting from a spontaneous collapse of elements of the ER tubular network adjacent to the ER sheet edge and calculated the nanohole dimensions. We proposed the ERES membrane to have a shape of a super flexible membrane bead chain, which acquires random walk configurations unless an ultra-low tension converts it into a straight conformation of a transport intermediate. The adequacy of the proposed concept is supported by a close qualitative and quantitative similarity between the predicted and observed configurations of all four ER nanostructures.

Evaluation of grain boundary energy, structure and stiffness from phase field crystal simulations

A two-mode phase field crystal (PFC) model is employed to investigate the equilibrium configurations of a range of grain boundaries in fcc-structured materials. A total of 80 different symmetrical tilt grain boundaries are evaluated by PFC simulations in 3D and the results are shown to agree well with data taken from the literature, both regarding the variation of grain boundary energy and also in terms of the resulting grain boundary structures. This verification complements existing PFC studies which are almost exclusively focused either on grain boundaries found in 2D systems or in bcc lattices in 3D. The present work facilitates application of PFC in the analysis of grain boundary mechanics in an extended range of materials, in particular such mechanics that take place at extended time scales not tractable for molecular dynamics (MD) simulations. In addition to the verification of predicted grain boundary energies and structures, wavelet transforms of the density field are used in the present work to obtain phase fields from which it is possible to identify grain boundary fluctuations that provide the means to evaluate grain boundary stiffness based on the capillarity fluctuation method. It is discussed how PFC provides benefits compared to alternative methods, such as MD simulations, for this type of investigations.

Liquid walls and interfaces in arbitrary directions stabilized by vibrations

Gravity shapes liquids and plays a crucial role in their internal balance. Creating new equilibrium configurations irrespective of the presence of a gravitational field is challenging with applications on Earth as well as in zero-gravity environments. Vibrations are known to alter the shape of liquid interfaces and also to change internal dynamics and stability in depth. Here, we show that vibrations can also create an “artificial gravity” in any direction. We demonstrate that a liquid can maintain an inclined interface when shaken in an arbitrary direction. A necessary condition for the equilibrium to occur is the existence of a velocity gradient determined by dynamical boundary conditions. However, the no-slip boundary condition and incompressibility can perturb the required velocity profile, leading to a destabilization of the equilibrium. We show that liquid layers provide a solution, and liquid walls of several centimeters in height can thus be stabilized. We show that the buoyancy equilibrium is not affected by the forcing.

Accessing Structural, Electronic, Transport and Mesoscale Properties of Li-GICs via a Complete DFTB Model with Machine-Learned Repulsion Potential

Lithium-graphite intercalation compounds (Li-GICs) are the most popular anode material for modern lithium-ion batteries and have been subject to numerous studies—both experimental and theoretical. However, the system is still far from being consistently understood in detail across the full range of state of charge (SOC). The performance of approaches based on density functional theory (DFT) varies greatly depending on the choice of functional, and their computational cost is far too high for the large supercells necessary to study dilute and non-equilibrium configurations which are of paramount importance for understanding a complete charging cycle. On the other hand, cheap machine learning methods have made some progress in predicting, e.g., formation energetics, but fail to provide the full picture, including electrostatics and migration barriers. Following up on our previous work, we deliver on the promise of providing a complete and affordable simulation framework for Li-GICs. It is based on density functional tight binding (DFTB), which is fitted to dispersion-corrected DFT data using Gaussian process regression (GPR). In this work, we added the previously neglected lithium–lithium repulsion potential and extend the training set to include superdense Li-GICs (LiC6−x; x>0) and lithium metal, allowing for the investigation of dendrite formation, next-generation modified GIC anodes, and non-equilibrium states during fast charging processes in the future. For an extended range of structural and energetic properties—layer spacing, bond lengths, formation energies and migration barriers—our method compares favorably with experimental results and with state-of-the-art dispersion-corrected DFT at a fraction of the computational cost. We make use of this by investigating some larger-scale system properties—long range Li–Li interactions, dielectric constants and domain-formation—proving our method’s capability to bring to light new insights into the Li-GIC system and bridge the gap between DFT and meso-scale methods such as cluster expansions and kinetic Monte Carlo simulations.

Anisotropic solution for compact star in 5D Einstein–Gauss–Bonnet gravity

In astronomy, the study of compact stellar remnants — white dwarfs, neutron stars, black holes — has attracted much attention for addressing fundamental principles of physics under extreme conditions in the core of compact objects. In a recent argument, Maurya et al. [Eur. Phys. J. C 77, 45 (2017)] have proposed an exact solution depending on a specific spacetime geometry. Here, we construct equilibrium configurations of compact stars for the same spacetime that make it interesting for modeling high density physical astronomical objects. All calculations are carried out within the framework of the five-dimensional Einstein–Gauss–Bonnet gravity. Our main interest is to explore the dependence of the physical properties of these compact stars depending on the Gauss–Bonnet coupling constant. The interior solutions have been matched to an exterior Boulware–Deser solution for [Formula: see text] spacetime. Our finding ensures that all energy conditions hold, and the speed of sound remains causal, everywhere inside the star. Moreover, we study the dynamical stability of stellar structure by taking into account the modified field equations using the theory of adiabatic radial oscillations developed by Chandrasekhar. Based on the observational data for radii and masses coming from different astronomical sources, we show that our model is compatible and physically relevant.

Global and Local Dynamics of a Bistable Asymmetric Composite Laminated Shell

As bistable composite laminated plate and shell structures are often exposed to dynamic environments in practical applications, the global and local dynamics of a bistable asymmetric composite laminated shell subjected to the base excitation is presented in this paper. Temperature difference, base excitation amplitude, and detuning parameters are discussed. With the change of temperature difference, the super-critical pitchfork bifurcation occurs. Three equilibrium solutions corresponding to three equilibrium configurations (two stable configurations and one unstable configuration) can be obtained. With the increase of excitation amplitude, local and global dynamics play a leading role successively. The global dynamics between the two stable configurations behave as the periodic vibration, the quasi-periodic vibration, the chaotic vibration and dynamic snap-through when the excitation amplitude is large enough. The local dynamics that are confined to a single stable configuration behave as 1:2 internal resonance, saturation and permeation when the excitation amplitude is small. Dynamic snap-through and large-amplitude vibrations with two potential wells for the global dynamics will lead to a broad application prospect of the bistable asymmetric composite laminated shell in energy harvesting devices.

Structures With Multiple Rigid Configurations Due to Prestress and Unilateral Contacts

This paper presents structures with multiple equilibrium configurations arising from the combination of a state of prestress and unilateral contacts. A design problem is posed where preloaded elastic springs and unilateral constraints are embedded throughout a mechanism. The spring parameters are designed such that multiple target configurations are immobilized due to contact. In each of these configurations, the spring forces maintain compressive reaction forces, immobilizing the structure. Each immobilized configuration can rigidly resist perturbation forces up to some finite magnitude where contact is lost. Hence, this case of multiple configurations in equilibrium due to the combination of prestress and contact is referred to as multi-configuration rigidity. Two examples of structures exhibiting multi-configuration rigidity are presented. First, a four bar linkage with a single kinematic degree of freedom is used to introduce the concept. In the context of the linkage, multi-configuration rigidity is compared to multi-stability, exhibiting the key differences between the two concepts. Then, a 24-degree-of-freedom kirigami surface is presented that can morph between flat and spherical configurations, motivated by RF antenna applications. By embedding torsional springs and fold angle stops throughout the structure, flat and spherical configurations are made rigid. Actuation between the configurations can easily be achieved by snapping the structure between the rigid configurations.

Chromonic liquid crystals and packing configurations of bacteriophage viruses

We study equilibrium configurations of hexagonal columnar liquid crystals in the context of characterizing packing structures of bacteriophage viruses in a protein capsid. These are viruses that infect bacteria and are currently the focus of intense research efforts, with the goal of finding new therapies for bacteria-resistant antibiotics. The energy that we propose consists of the Oseen–Frank free energy of nematic liquid crystals that penalizes bending of the columnar directions, in addition to the cross-sectional elastic energy accounting for distortions of the transverse hexagonal structure; we also consider the isotropic contribution of the core and the energy of the unknown interface between the outer ordered region of the capsid and the inner disordered core. The problem becomes of free boundary type, with constraints. We show that the concentric, azimuthal, spool-like configuration is the absolute minimizer. Moreover, we present examples of toroidal structures formed by DNA in free solution and compare them with the analogous ones occurring in experiments with other types of lyotropic liquid crystals, such as food dyes and additives. This article is part of the theme issue ‘Topics in mathematical design of complex materials’.