Minimal Model System Research Articles

Loss of memory of an elastic line on its way to limit cycles.

Oscillatory-driven amorphous materials forget their initial configuration and converge to limit cycles. Here we investigate this memory loss under a nonquasistatic drive in a minimal model system, with quenched disorder and memory encoded in a spatial pattern, where oscillating protocols are formally replaced by a positive-velocity drive. We consider an elastic line driven athermally in a quenched disorder with biperiodic boundary conditions and tunable system size, thus controlling the area swept by the line per cycle as would the oscillation amplitude. The convergence to disorder-dependent limit cycle is strongly coupled to the nature of its velocity dynamics depending on system size. Based on the corresponding phase diagram, we propose a generic scenario for memory formation in disordered systems under finite driving rate.

Reconstitution of cytolinker-mediated crosstalk between actin and vimentin

Cell shape and motility are determined by the cytoskeleton, an interpenetrating network of actin filaments, microtubules, and intermediate filaments. The biophysical properties of each filament type individually have been studied extensively by cell-free reconstitution. By contrast, the interactions between the three cytoskeletal networks are relatively unexplored. They are coupled via crosslinkers of the plakin family such as plectin. These are challenging proteins for reconstitution because of their giant size and multidomain structure. Here we engineer a recombinant actin-vimentin crosslinker protein called ‘ACTIF’ that provides a minimal model system for plectin, recapitulating its modular design with actin-binding and intermediate filament-binding domains separated by a coiled-coil linker for dimerisation. We show by fluorescence and electron microscopy that ACTIF has a high binding affinity for vimentin and actin and creates mixed actin-vimentin bundles. Rheology measurements show that ACTIF-mediated crosslinking strongly stiffens actin-vimentin composites. Finally, we demonstrate the modularity of this approach by creating an ACTIF variant with the intermediate filament binding domain of Adenomatous Polyposis Coli. Our protein engineering approach provides a new cell-free system for the biophysical characterization of intermediate filament-binding crosslinkers and for understanding the mechanical synergy between actin and vimentin in mesenchymal cells.

Optimizing the random search of a finite-lived target by a Lévy flight.

In many random search processes of interest in chemistry, biology, or during rescue operations, an entity must find a specific target site before the latter becomes inactive, no longer available for reaction or lost. We present exact results on a minimal model system, a one-dimensional searcher performing a discrete time random walk, or Lévy flight. In contrast with the case of a permanent target, the capture probability and the conditional mean first passage time can be optimized. The optimal Lévy index takes a nontrivial value, even in the long lifetime limit, and exhibits an abrupt transition as the initial distance to the target is varied. Depending on the target lifetime, this transition is discontinuous or continuous, separated by a nonconventional tricritical point. These results pave the way to the optimization of search processes under time constraints.

Force propagation between epithelial cells depends on active coupling and mechano-structural polarization.

Cell-generated forces play a major role in coordinating the large-scale behavior of cell assemblies, in particular during development, wound healing, and cancer. Mechanical signals propagate faster than biochemical signals, but can have similar effects, especially in epithelial tissues with strong cell-cell adhesion. However, a quantitative description of the transmission chain from force generation in a sender cell, force propagation across cell-cell boundaries, and the concomitant response of receiver cells is missing. For a quantitative analysis of this important situation, here we propose a minimal model system of two epithelial cells on an H-pattern ('cell doublet'). After optogenetically activating RhoA, a major regulator of cell contractility, in the sender cell, we measure the mechanical response of the receiver cell by traction force and monolayer stress microscopies. In general, we find that the receiver cells show an active response so that the cell doublet forms a coherent unit. However, force propagation and response of the receiver cell also strongly depend on the mechano-structural polarization in the cell assembly, which is controlled by cell-matrix adhesion to the adhesive micropattern. We find that the response of the receiver cell is stronger when the mechano-structural polarization axis is oriented perpendicular to the direction of force propagation, reminiscent of the Poisson effect in passive materials. We finally show that the same effects are at work in small tissues. Our work demonstrates that cellular organization and active mechanical response of a tissue are key to maintain signal strength and lead to the emergence of elasticity, which means that signals are not dissipated like in a viscous system, but can propagate over large distances.

Another Torture Track for Quantum Chemistry: Reinvestigation of the Benzaldehyde Amidation by Nitrogen‐Atom Transfer from Platinum(II) and Palladium(II) Metallonitrenes

AbstractWe showcase here a dramatic failure of CCSD(T) theory that originates from the pronounced multi‐reference character of a key intermediate formed in the benzaldehyde amidation by N‐atom transfer from Pd(II) and Pt(II) metallonitrenes studied recently in combined experimental and theoretical work. For detailed analysis we devised a minimal model system, for which we established reliable reference energies based on approximate full configuration interaction theory, to assess the performance of single‐reference coupled‐cluster theory up to the CCSDTQ(P) excitation level. While RHF‐based CCSD(T) theory suffered dramatic errors, in one case exceeding 220 kcal mol−1, we show that the use of broken‐symmetry (BS) or Kohn‐Sham (KS) orbital references yields substantially improved CCSD(T) results. Further, the EOM‐SF‐CCSD(T)(a)* approach met the reference data with excellent accuracy. We applied the KS‐CCSD(T*)‐F12b variant as high‐level part of an ONIOM(KS‐CC:DFT) scheme to reinvestigate the reactivity of the full Pt(II) and Pd(II) metallonitrenes. The revised reaction pathway energetics provide a detailed mechanistic rationale for the experimental observations.

Investigating the structural and dynamical basis for ion affinity in the ion-binding sites of signaling proteins.

Calcium binding in proteins is essential to numerous biological processes including signaling and homeostasis. EF-hands are one of the most widely-studied Ca2+ binding motifs. These highly-conserved motifs are found in signaling proteins, but despite numerous studies the relationship between sequence, conformational ensembles, and affinities is not well understood. To investigate EF-hand motifs, Lanthanides are commonly used as biophysically-tractable substitute for Ca2+ because the lanthanides provide a direct handle on ionic radius, thus enabling characterization of the protein response to changes in ion size. Here we seek to understand the sequence-structure relation in EF-hands to obtain a structural basis that will explain the sequence-affinity relation observed in nature and connect the response of EF-hands to global conformational changes in signaling proteins. Two-dimensional infrared (2D IR) spectroscopy and MD simulations are used to monitor the EF Hand motifs ability to bind to lanthanides outside the protein scaffold, as a minimal model system, and the changes in the secondary structure of each EF Hand motif in lanthanide metal solutions. The results show that the sequence of the EF Hand motifs plays a crucial role in the ability of the motif to bind to ions of specific radius. A single mutation of the EF Hand motif resulted in the following behavior: no binding, preferential binding to smaller ionic radii (<95 pm), and binding to a range of ionic radii (86-105 pm). The results are interpreted through simulations, which connect measured spectra to specific changes in the configurational ensembles.

Exploring generic principles of compartmentalization in a developmental in vitro model.

Self-organization of cells into higher-order structures is key for multicellular organisms, for example via repetitive replication of template-like founder cells or syncytial energids. Yet, very similar spatial arrangements of cell-like compartments ('protocells') are also seen in a minimal model system of Xenopus egg extracts in the absence of template structures and chromatin, with dynamic microtubule assemblies driving the self-organization process. Quantifying geometrical features over time, we show here that protocell patterns are highly organized with a spatial arrangement and coarsening dynamics similar to that of two-dimensional foams but without the long-range ordering expected for hexagonal patterns. These features remain invariant when enforcing smaller protocells by adding taxol, i.e. patterns are dominated by a single, microtubule-derived length scale. Comparing our data to generic models, we conclude that protocell patterns emerge by simultaneous formation of randomly assembling protocells that grow at a uniform rate towards a frustrated arrangement before fusion of adjacent protocells eventually drives coarsening. The similarity of protocell patterns to arrays of energids and cells in developing organisms, but also to epithelial monolayers, suggests generic mechanical cues to drive self-organized space compartmentalization.

Extracellular Cues Govern Shape and Cytoskeletal Organization in Giant Unilamellar Lipid Vesicles.

Spontaneous and induced front-rear polarization and a subsequent asymmetric actin cytoskeleton is a crucial event leading to cell migration, a key process involved in a variety of physiological and pathological conditions such as tissue development, wound healing, and cancer. Migration of adherent cells relies on the balance between adhesion to the underlying matrix and cytoskeleton-driven front protrusion and rear retraction. A current challenge is to uncouple the effect of adhesion and shape from the contribution of the cytoskeleton in regulating the onset of front-rear polarization. Here, we present a minimal model system that introduces an asymmetric actin cytoskeleton in synthetic cells, which are resembled by giant unilamellar lipid vesicles (GUVs) adhering onto symmetric and asymmetric micropatterned surfaces. Surface micropatterning of streptavidin-coated regions with varying adhesion shape and area was achieved by maskless UV photopatterning. To further study the effects of GUV shape on the cytoskeletal organization, actin filaments were polymerized together with bundling proteins inside the GUVs. The micropatterns induce synthetic cell deformation upon adhesion to the surface, with the cell shape adapting to the pattern shape and size. As expected, asymmetric patterns induce an asymmetric deformation in adherent synthetic cells. Actin filaments orient along the long axis of the deformed GUV, when having a length similar to the size of the major axis, whereas short filaments exhibit random orientation. With this bottom-up approach we have laid the first steps to identify the relationship between cell front-rear polarization and cytoskeleton organization in the future. Such a minimal system will allow us to further study the major components needed to create a polarized cytoskeleton at the onset of migration.

Phase separation in amino acid mixtures is governed by composition

Macromolecular phase separation has recently come to immense prominence as it is central to the formation of membraneless organelles, leading to a new paradigm of cellular organization. This type of phase transition, often termed liquid-liquid phase separation (LLPS), is mediated by molecular interactions between biomolecules, including nucleic acids and both ordered and disordered proteins. In the latter case, the separation between protein-dense and -dilute phases is often interpreted using models adapted from polymer theory. Specifically, the “stickers and spacers” model proposes that the formation of condensate-spanning networks in protein solutions originates from the interplay between two classes of residues and that the main determinants for phase separation are multivalency and sequence patterning. The duality of roles of stickers (aromatics like Phe and Tyr) and spacers (Gly and polar residues) may apply more broadly in protein-like mixtures, and the presence of these two types of components alone may suffice for LLPS to take place. In order to explore this hypothesis, we use atomistic molecular dynamics simulations of capped amino acid residues as a minimal model system. We study the behavior of pure amino acids in water for three types of residues corresponding to the spacer and sticker categories and of their multicomponent mixtures. In agreement with previous observations, we find that the spacer-type amino acids fail to phase separate on their own, while the sticker is prone to aggregation. However, ternary amino acid mixtures involving both types of amino acids phase separate into two phases that retain intermediate degrees of compaction and greater fluidity than sticker-only condensates. Our results suggest that LLPS is an emergent property of amino acid mixtures determined by composition.

Self-assembly of emulsion droplets through programmable folding.

In the realm of particle self-assembly, it is possible to reliably construct nearly arbitrary structures if all the pieces are distinct1-3, but systems with fewer flavours of building blocks have so far been limited to the assembly of exotic crystals4-6. Here we introduce a minimal model system of colloidal droplet chains7, with programmable DNA interactions that guide their downhill folding into specific geometries. Droplets are observed in real space and time, unravelling the rules of folding. Combining experiments, simulations and theory, we show that controlling the order in which interactions are switched on directs folding into unique structures, which we call colloidal foldamers8. The simplest alternating sequences (ABAB...) of up to 13 droplets yield 11 foldamers in two dimensions and one in three dimensions. Optimizing the droplet sequence and adding an extra flavour uniquely encodes more than half of the 619 possible two-dimensional geometries. Foldamers consisting of at least 13 droplets exhibit open structures with holes, offering porous design. Numerical simulations show that foldamers can further interact to make complex supracolloidal architectures, such as dimers, ribbons and mosaics. Our results are independent of the dynamics and therefore apply to polymeric materials with hierarchical interactions on all length scales, from organic molecules all the way to Rubik's Snakes. This toolbox enables the encoding of large-scale design into sequences of short polymers, placing folding at the forefront of materials self-assembly.

Revealing and Controlling Energy Barriers and Valleys at Grain Boundaries in Ultrathin Organic Films.

In organic electronics, local crystalline order is of critical importance for the charge transport. Grain boundaries between molecularly ordered domains are generally known to hamper or completely suppress charge transfer and detailed knowledge of the local electronic nature is critical for future minimization of such malicious defects. However, grain boundaries are typically hidden within the bulk film and consequently escape observation or investigation. Here, a minimal model system in form of monolayer-thin films with sub-nm roughness of a prototypical n-type organic semiconductor is presented. Since these films consist of large crystalline areas, the detailed energy landscape at single grain boundaries can be studied using Kelvin probe force microscopy. By controlling the charge-carrier density in the films electrostatically, the impact of the grain boundaries on charge transport in organic devices is modeled. First, two distinct types of grain boundaries are identified, namely energetic barriers and valleys, which can coexist within the same thin film. Their absolute height is found to be especially pronounced at charge-carrier densities below 1012 cm- 2 -the regime at which organic solar cells and light emitting diodes typically operate. Finally, processing conditions by which the type or energetic height of grain boundaries can be controlled are identified.

Collective dynamics of capacity-constrained ride-pooling fleets

Ride-pooling (or ride-sharing) services combine trips of multiple customers along similar routes into a single vehicle. The collective dynamics of the fleet of ride-pooling vehicles fundamentally underlies the efficiency of these services. In simplified models, the common features of these dynamics give rise to scaling laws of the efficiency that are valid across a wide range of street networks and demand settings. However, it is unclear how constraints of the vehicle fleet impact such scaling laws. Here, we map the collective dynamics of capacity-constrained ride-pooling fleets to services with unlimited passenger capacity and identify an effective fleet size of available vehicles as the relevant scaling parameter characterizing the dynamics. Exploiting this mapping, we generalize the scaling laws of ride-pooling efficiency to capacity-constrained fleets. We approximate the scaling function with a queueing theoretical analysis of the dynamics in a minimal model system, thereby enabling mean-field predictions of required fleet sizes in more complex settings. These results may help to transfer insights from existing ride-pooling services to new settings or service locations.

Photoinducible Azobenzene trimethylammonium bromide (AzoTAB)-mediated giant vesicle fusion compatible with synthetic protein translation reactions

Lipid giant vesicles represent a versatile minimal model system to study the physicochemical basis of lipid membrane fusion. Membrane fusion processes are also of interest in synthetic cell research, where cell-mimicking behavior often requires dynamically interacting compartments. For these applications, triggered fusion compatible with transcription-translation systems is key in achieving complexity. Recently, a photosensitive surfactant, azobenzene trimethylammonium bromide (AzoTAB), has been reported to induce membrane fusion by a photoinduced conformational change. Using imaging flow cytometer (IFC) and confocal microscopy we quantitatively investigated photoinduced AzoTAB-mediated fusion of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine vesicles. The IFC analysis result showed that the fusion rate could reach about 40% following AzoTAB addition and UV irradiation in optimized conditions. We confirmed the compatibility between AzoTAB-induced vesicle fusion and a synthetic cell-free protein translation system using green fluorescent protein as reporter. With the techniques presented, cell-sized vesicle fusion can be quantitatively analyzed and optimized, paving the way to controllable synthetic cells with fundamental biological functions like the ability to express proteins from encapsulated plasmids.

Structure and Energetics of GTP- and GDP-Tubulin Isodesmic Self-Association.

Tubulin self-association is a critical process in microtubule dynamics. The early intermediate structures, energetics, and their regulation by fluxes of chemical energy, associated with guanosine triphosphate (GTP) hydrolysis, are poorly understood. We reconstituted an in vitro minimal model system, mimicking the key elements of the nontemplated tubulin assembly. To resolve the distribution of GTP- and guanosine diphosphate (GDP)-tubulin structures, at low temperatures (∼10 °C) and below the critical concentration for the microtubule assembly, we analyzed in-line size-exclusion chromatography-small-angle X-ray scattering (SEC-SAXS) chromatograms of GTP- and GDP-tubulin solutions. Both solutions rapidly attained steady state. The SEC-SAXS data were consistent with an isodesmic thermodynamic model of longitudinal tubulin self-association into 1D oligomers, terminated by the formation of tubulin single rings. The analysis showed that free dimers coexisted with tetramers and hexamers. Tubulin monomers and lateral association between dimers were not detected. The dimer-dimer longitudinal self-association standard Helmholtz free energies were -14.2 ± 0.4 kBT (-8.0 ± 0.2 kcal mol-1) and -13.1 ± 0.5 kBT (-7.4 ± 0.3 kcal mol-1) for GDP- and GTP-tubulin, respectively. We then determined the mass fractions of dimers, tetramers, and hexamers as a function of the total tubulin concentration. A small fraction of stable tubulin single rings, with a radius of 19.2 ± 0.2 nm, was detected in the GDP-tubulin solution. In the GTP-tubulin solution, this fraction was significantly lower. Cryo-TEM images and SEC-multiangle light-scattering analysis corroborated these findings. Our analyses provide an accurate structure-stability description of cold tubulin solutions.

Mitochondrial Cristae Architecture and Functions: Lessons from Minimal Model Systems.

Mitochondria are known as the powerhouse of eukaryotic cells. Energy production occurs in specific dynamic membrane invaginations in the inner mitochondrial membrane called cristae. Although the integrity of these structures is recognized as a key point for proper mitochondrial function, less is known about the mechanisms at the origin of their plasticity and organization, and how they can influence mitochondria function. Here, we review the studies which question the role of lipid membrane composition based mainly on minimal model systems.

Lipid Bilayer Passive Area Regulation in Response to Fluid Flows

Mechanotransduction is the cellular process in which mechanical stimuli are converted into biochemical signals to induce specific cellular responses, enabling the cell to sense and respond to mechanical forces. Although many cells exhibit this behavior, vascular endothelial cells (ECs) are of considerable interest as they effectively respond to fluid shear stress, adapting their morphology, functions and gene expression to maintain the homeostasis of the vascular system. Fundamentally, these processes rely on the transduction of intracellular signals through the lipid membrane, and several studies have already demonstrated that shear stress induces significant changes in lipid order and viscosity of ECs plasma membrane. Despite such extensive study, the underlying molecular mechanisms that control this change to membrane lipid order and viscosity remain unclear. Supported lipid bilayers provide an ideal platform for the investigation of the molecular mechanisms behind shear induced biophysical changes in membrane structure. As a minimal model system, they are suited for isolating the physical role of lipid bilayer in membrane shear response, in the absence of active biological processes. Here, combining microfluidics and fluorescence microscopy, we examine how the application of controlled fluid flows on supported lipid bilayer patches alters their physical properties. We observe a reversible and significant ∼10% increase in SLB area (when physiological shear stresses of 1-2 Pa are applied). Such area fluctuations have been a previously suggested response to fluid shear stress but have not directly observed. Furthermore, we determine how these membrane area fluctuations in response to fluid flows depend on lipid composition and surface roughness. Identifying the origin of such flow-induced changes in membrane structure could reveal an underlying mechanism utilized by biology to sense and direct changes in membrane order and viscosity in response to shear flows.

Active particles induce large shape deformations in giant lipid vesicles.

Biological cells generate intricate structures by sculpting their membrane from within to actively sense and respond to external stimuli or to explore their environment1-4. Several pathogenic bacteria also provide examples of how localized forces strongly deform cell membranes from inside, leading to the invasion of neighbouring healthy mammalian cells5. Giant unilamellar vesicles have been successfully used as a minimal model system with which to mimic biological cells6-11, but the realization of a minimal system with localized active internal forces that can strongly deform lipid membranes from within and lead to dramatic shape changes remains challenging. Here we present a combined experimental and simulation study that demonstrates how self-propelled particles enclosed in giant unilamellar vesicles can induce a plethora of non-equilibrium shapes and active membrane fluctuations. Using confocal microscopy,in the experiments weexplore the membrane response to local forces exerted by self-phoretic Janusmicroswimmers. To quantify dynamic membrane changes,we perform Langevin dynamics simulations of active Brownian particles enclosed in thin membrane shells modelled by dynamically triangulated surfaces. The most pronounced shape changes are observed at low and moderate particle loadings, with the formation of tether-like protrusions and highly branched, dendritic structures, whereas at high volume fractions globally deformed vesicle shapes are observed. The resulting state diagram predicts the conditions under which local internal forces generate various membrane shapes. A controlled realization of such distorted vesicle morphologies could improve the design of artificial systems such as small-scale soft robots and synthetic cells.

Solution structure and RNA-binding of a minimal ProQ-homolog from Legionella pneumophila (Lpp1663).

Small regulatory RNAs (sRNAs) play an important role for posttranscriptional gene regulation in bacteria. sRNAs recognize their target messenger RNAs (mRNAs) by base-pairing, which is often facilitated by interactions with the bacterial RNA-binding proteins Hfq or ProQ. The FinO/ProQ RNA-binding protein domain was first discovered in the bacterial repressor of conjugation, FinO. Since then, the functional role of FinO/ProQ-like proteins in posttranscriptional gene regulation was extensively studied in particular in the enterobacteria E. coli and Salmonella enterica and a wide range of sRNA-targets was identified for these proteins. In addition, enterobacterial ProQ homologs also recognize and protect the 3′-ends of a number of mRNAs from exonucleolytic degradation. However, the RNA-binding properties of FinO/ProQ proteins with regard to the recognition of different RNA targets are not yet fully understood. Here, we present the solution NMR structure of the so far functionally uncharacterized ProQ homolog Lpp1663 from Legionella pneumophila as a newly confirmed member and a minimal model system of the FinO/ProQ protein family. In addition, we characterize the RNA-binding preferences of Lpp1663 with high resolution NMR spectroscopy and isothermal titration calorimetry (ITC). Our results suggest a binding preference for single-stranded uridine-rich RNAs in the vicinity of stable stem–loop structures. According to chemical shift perturbation experiments, the single-stranded U-rich RNAs interact mainly with a conserved RNA-binding surface on the concave site of Lpp1663.

The Relationship between Effective Molarity and Affinity Governs Rate Enhancements in Tethered Kinase-Substrate Reactions.

Scaffold proteins are thought to accelerate protein phosphorylation reactions by tethering kinases and substrates together, but there is little quantitative data on their functional effects. To assess the contribution of tethering to kinase reactivity, we compared intramolecular and intermolecular kinase reactions in a minimal model system. We found that tethering can enhance reaction rates in a flexible tethered kinase system and that the magnitude of the effect is sensitive to the structure of the tether. The largest effective molarity we obtained was ∼0.08 μM, which is much lower than the effects observed in small molecule model systems and other tethered protein reactions. We further demonstrated that the tethered intramolecular reaction only makes a significant contribution to the observed rates when the scaffolded complex assembles at concentrations below the effective molarity. These findings provide a quantitative framework that can be applied to understand endogenous protein scaffolds and engineer synthetic networks.

MCTDH-X: The multiconfigurational time-dependent Hartree method for indistinguishable particles software

We introduce and describe the multiconfigurational time-depenent Hartree for indistinguishable particles (MCTDH-X) software, which is hosted, documented, and distributed at http://ultracold.org. This powerful tool allows the investigation of ground state properties and dynamics of interacting quantum many-body systems in different spatial dimensions. The MCTDH-X software is a set of programs and scripts to compute, analyze, and visualize solutions for the time-dependent and time-independent many-body Schrödinger equation for indistinguishable quantum particles. As the MCTDH-X software represents a general solver for the Schrödinger equation, it is applicable to a wide range of problems in the fields of atomic, optical, molecular physics, and condensed matter systems. In particular, it can be used to study light–matter interactions, correlated dynamics of electrons in the solid state as well as some aspects related to quantum information and computing. The MCTDH-X software solves a set of nonlinear coupled working equations based on the application of the time-dependent variational principle to the Schrödinger equation. These equations are obtained by using an ansatz for the many-body wavefunction that is a expansion in a set of time-dependent, fully symmetrized bosonic (X = B) or fully anti-symmetrized fermionic (X = F) many-body basis states. It is the time-dependence of the basis set that enables MCTDH-X to deal with quantum dynamics at a superior accuracy as compared to, for instance, exact diagonalization approaches with a static basis, where the number of basis states necessary to capture the dynamics of the wavefunction typically grows rapidly with time. Herein, we give an introduction to the MCTDH-X software via an easy-to-follow tutorial with a focus on accessibility. The illustrated exemplary problems are hosted at http://ultracold.org/tutorial and consider the physics of a few interacting bosons or fermions in a double-well potential. We explore computationally the position-space and momentum-space density, the one-body reduced density matrix, Glauber correlation functions, phases, (dynamical) phase transitions, and the imaging of the quantum systems in single-shot images. Although a few particles in a double well potential represent a minimal model system, we are able to demonstrate a rich variety of phenomena with it. We use the double well to illustrate the fermionization of bosonic particles, the crystallization of fermionic particles, characteristics of the superfluid and Mott-insulator quantum phases in Hubbard models, and even dynamical phase transitions. We provide a complete set of input files and scripts to redo all computations in this paper at http://ultracold.org/data/tutorial_input_files.zip, accompanied by tutorial videos at https://tinyurl.com/tjx35sq. Our tutorial should guide the potential users to apply the MCTDH-X software also to more complex systems.