Elastic properties of mono- and polydisperse two-dimensional crystals of hard--core repulsive Yukawa particles

Monte Carlo simulations of mono-- and polydisperse two--dimensional crystals are reported. The particles in the studied system, interacting through hard--core repulsive Yukawa potential, form a solid phase of hexagonal lattice. The elastic properties of crystalline Yukawa systems are determined in the $NpT$ ensemble with variable shape of the periodic box. Effects of the Debye screening length ($\kappa^{-1}$), contact value of the potential ($\epsilon$), and the size polydispersity of particles on elastic properties of the system are studied. The simulations show that the polydispersity of particles strongly influences the elastic properties of the studied system, especially on the shear modulus. It is also found that the elastic moduli increase with density and their growth rate depends on the screening length. Shorter screening length leads to faster increase of elastic moduli with density and decrease of the Poisson's ratio. In contrast to its three-dimensional version, the studied system is non-auxetic, i.e. shows positive Poisson's ratio

AmyloGraph : a comprehensive database of amyloid-amyloid interactions

Information about the impact of interactions between amyloid proteins on their fibrillization propensity is scattered among many experimental articles and presented in unstructured form. We manually curated information located in almost 200 publications (selected out of 562 initially considered), obtaining details of 883 experimentally studied interactions between 46 amyloid proteins or peptides. We also proposed a novel standardized terminology for the description of amyloid-amyloid interactions, which is included in our database, covering all currently known types of such a cross-talk, including inhibition of fibrillization, cross-seeding and other phenomena. The new approach allows for more specific studies on amyloids and their interactions, by providing very well-defined data. AmyloGraph, an online database presenting information on amyloid-amyloid interactions, is available at (). Its functionalities are also accessible as the R package (). AmyloGraph is the only publicly available repository for experimentally determined amyloid-amyloid interactions

Poisson’s Ratio of the f.c.c. Hard Sphere Crystals with Periodically Stacked (001)-Nanolayers of Hard Spheres of Another Diameter

The results of studies on the influence of periodically stacked nanolayer inclusions, introduced into the face-centered cubic (f.c.c.) hard sphere crystal, on Poisson’s ratio of the obtained nanocomposite system are presented. The monolayers are orthogonal to the [ 001 ] -direction. They are formed by hard spheres with diameter different from the spheres forming the matrix of the system. The Monte Carlo computer simulations show that in such a case the symmetry of the system changes from the cubic to tetragonal one. When the diameter of the inclusion spheres increases at certain range, a decrease of the negative Poisson’s ratio in the [ 101 ] [ 1 ¯ 01 ] -directions is observed, i.e., the system enhances its partial auxeticity. The dependence of the maximal, average, and negative parts of the minimal Poisson’s ratio on the direction of the applied load are shown in a form of surfaces in spherical coordinates, plotted for selected values of nanolayer particle diameters. The most negative value of the Poisson’s ratio found among all studied systems was − 0.11 (at pressure p * = 100 , which is about ten times higher than the melting pressure) what is almost twice more negative than in the f.c.c. crystal of identical hard spheres. The observed effect weakens along with the decrease of pressure and becomes hardly noticeable near melting. This study indicates that modifying only the size of the inclusion particles one can change Poisson’s ratio of nanocomposites at high pressures

Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools

To successfully design and optimize the application of hydrogel matrices one has to effectively combine computational design tools with experimental methods. In this context, one of the most promising techniques is molecular modeling, which requires however accurate molecular models representing the investigated material. Although this method has been successfully used over the years for predicting the properties of polymers, its application to biopolymers, including gelatin, is limited. In this paper we provide a method for creating an atomistic representation of gelatin based on the modified FASTA codes of natural collagen. We show that the model created in this manner reproduces known experimental values of gelatin properties like density, glass-rubber transition temperature, WAXS profile and isobaric thermal expansion coefficient. We also present that molecular dynamics using the INTERFACE force field provides enough accuracy to track changes of density, fractional free volume and Hansen solubility coefficient over a narrow temperature regime (273–318 K) with 1 K accuracy. Thus we depict that using molecular dynamics one can predict properties of gelatin biopolymer as an efficient matrix for immobilization of various bioactive compounds, including enzymes

Pressure-Volume Work for Metastable Liquid and Solid at Zero Pressure

Unlike with gases, for liquids and solids the pressure of a system can be not only positive, but also negative, or even zero. Upon isobaric heat exchange (heating or cooling) at p = 0, the volume work (p-V) should be zero, assuming the general validity of traditional δW = dWp = −pdV equality. This means that at zero pressure, a special process can be realized; a macroscopic change of volume achieved by isobaric heating/cooling without any work done by the system on its surroundings or by the surroundings on the system. A neologism is proposed for these dWp = 0 (and in general, also for non-trivial δW = 0 and W = 0) processes: “aergiatic” (from Greek: Ἀεργία, “inactivity”). In this way, two phenomenologically similar processes—adiabatic without any heat exchange, and aergiatic without any work—would have matching, but well-distinguishable terms

High Partial Auxeticity Induced by Nanochannels in [111]-Direction in a Simple Model with Yukawa Interactions

Computer simulations using Monte Carlo method in the isobaric-isothermal ensemble were used to investigate the impact of nanoinclusions in the form of very narrow channels in the [ 111 ] -direction on elastic properties of crystals, whose particles interact via Yukawa potential. The studies were performed for several selected values of Debye screening length ( ( κ σ ) − 1 ). It has been observed that introduction of the nanoinclusions into the system reduces the negative value of Poisson’s ratio towards [ 110 ] [ 1 1 ¯ 0 ] , maintaining practically constant values of Poisson’s ratio in the directions [ 100 ] and [ 111 ] . These studies also show that concentration of particles forming the nanoinclusions in the system has a significant effect on the value of Poisson’s ratio in the [ 110 ] [ 1 1 ¯ 0 ] -direction. A strong (more than fourfold) decrease of Poisson’s ratio in this direction was observed, from − 0.147 ( 3 ) (system without inclusions) to − 0.614 ( 14 ) (system with nanoinclusions) at κ σ = 10 when the inclusion particles constituted about 10 percent of all particles. The research also showed an increase in the degree of auxeticity in the system with increasing concentration of nanoinclusion particles for all the screening lengths considered

Auxeticity of Yukawa Systems with Nanolayers in the (111) Crystallographic Plane

Elastic properties of model crystalline systems, in which the particles interact via the hard potential (infinite when any particles overlap and zero otherwise) and the hard-core repulsive Yukawa interaction, were determined by Monte Carlo simulations. The influence of structural modifications, in the form of periodic nanolayers being perpendicular to the crystallographic axis [111], on auxetic properties of the crystal was investigated. It has been shown that the hard sphere nanolayers introduced into Yukawa crystals allow one to control the elastic properties of the system. It has been also found that the introduction of the Yukawa monolayers to the hard sphere crystal induces auxeticity in the [ 11 1 ¯ ] [ 112 ] -direction, while maintaining the negative Poisson’s ratio in the [ 110 ] [ 1 1 ¯ 0 ] -direction, thus expanding the partial auxeticity of the system to an additional important crystallographic direction

Cancellation of Auxetic Properties in F.C.C. Hard Sphere Crystals by Hybrid Layer-Channel Nanoinclusions Filled by Hard Spheres of Another Diameter

The elastic properties of f.c.c. hard sphere crystals with periodic arrays of nanoinclusions filled by hard spheres of another diameter are the subject of this paper. It has been shown that a simple modification of the model structure is sufficient to cause very significant changes in its elastic properties. The use of inclusions in the form of joined (mutually orthogonal) layers and channels showed that the resulting tetragonal system exhibited a complete lack of auxetic properties when the inclusion spheres reached sufficiently large diameter. Moreover, it was very surprising that this hybrid inclusion, which can completely eliminate auxeticity, was composed of components that, alone, in these conditions, enhanced the auxeticity either slightly (layer) or strongly (channel). The study was performed with computer simulations using the Monte Carlo method in the isothermal-isobaric (NpT) ensemble with a variable box shape

Removing Auxetic Properties in f.c.c. Hard Sphere Crystals by Orthogonal Nanochannels with Hard Spheres of Another Diameter

Negative Poisson’s ratio materials (called auxetics) reshape our centuries-long understanding of the elastic properties of materials. Their vast set of potential applications drives us to search for auxetic properties in real systems and to create new materials with those properties. One of the ways to achieve the latter is to modify the elastic properties of existing materials. Studying the impact of inclusions in a crystalline lattice on macroscopic elastic properties is one of such possibilities. This article presents computer studies of elastic properties of f.c.c. hard sphere crystals with structural modifications. The studies were performed with numerical methods, using Monte Carlo simulations. Inclusions take the form of periodic arrays of nanochannels filled by hard spheres of another diameter. The resulting system is made up of two types of particles that differ in size. Two different layouts of mutually orthogonal nanochannels are considered. It is shown that with careful choice of inclusions, not only can one impact elastic properties by eliminating auxetic properties while maintaining the effective cubic symmetry, but also one can control the anisotropy of the cubic system