Jan Zidek

Accurate micro-computed tomography imaging of pore spaces in collagen-based scaffold

In this work we have used X-ray micro-computed tomography (μCT) as a method to observe the morphology of 3D porous pure collagen and collagen-composite scaffolds useful in tissue engineering. Two aspects of visualizations were taken into consideration: improvement of the scan and investigation of its sensitivity to the scan parameters. Due to the low material density some parts of collagen scaffolds are invisible in a μCT scan. Therefore, here we present different contrast agents, which increase the contrast of the scanned biopolymeric sample for μCT visualization. The increase of contrast of collagenous scaffolds was performed with ceramic hydroxyapatite microparticles (HAp), silver ions (Ag+) and silver nanoparticles (Ag-NPs). Since a relatively small change in imaging parameters (e.g. in 3D volume rendering, threshold value and μCT acquisition conditions) leads to a completely different visualized pattern, we have optimized these parameters to obtain the most realistic picture for visual and qualitative evaluation of the biopolymeric scaffold. Moreover, scaffold images were stereoscopically visualized in order to better see the 3D biopolymer composite scaffold morphology. However, the optimized visualization has some discontinuities in zoomed view, which can be problematic for further analysis of interconnected pores by commonly used numerical methods. Therefore, we applied the locally adaptive method to solve discontinuities issue. The combination of contrast agent and imaging techniques presented in this paper help us to better understand the structure and morphology of the biopolymeric scaffold that is crucial in the design of new biomaterials useful in tissue engineering.

Dynamic behavior of acrylic acid clusters as quasi-mobile nodes in a model of hydrogel network

Using a molecular dynamics simulation, we study the thermo-mechanical behavior of a model hydrogel subject to deformation and change in temperature. The model is found to describe qualitatively poly-lactide-glycolide hydrogels in which acrylic acid (AA)-groups are believed to play the role of quasi-mobile nodes in the formation of a network. From our extensive analysis of the structure, formation, and disintegration of the AA-groups, we are able to elucidate the relationship between structure and viscous-elastic behavior of the model hydrogel. Thus, in qualitative agreement with observations, we find a softening of the mechanical response at large deformations, which is enhanced by growing temperature. Several observables as the non-affinity parameter A and the network rearrangement parameter V indicate the existence of a (temperature-dependent) threshold degree of deformation beyond which the quasi-elastic response of the model system turns over into plastic (ductile) one. The critical stretching when the affinity of the deformation is lost can be clearly located in terms of A and V as well as by analysis of the energy density of the system. The observed stress-strain relationship matches that of known experimental systems.

Relaxation Mechanisms of Physical Hydrogels Networks

We study the dynamic mechanical behavior of a model hydrogel subject to deformation by means of Molecular Dynamics simulation. The model has a predefined invariable chemical composition and secondary structure of entangled network, but its macroscopic response to tensile deformation varies depending on external conditions. Our model has temperature-, pH, swelling degree-, and deformation rate-responsive behavior. The model is found to respond to changes in external conditions qualitatively in the same way as real hydrogels, which serve as reference in our study. The model is focused on physical hydrogels, where the self-assembly of interacting acrylic acid (AA)-groups plays essential role in the formation of the network. In particular, as a modeled material we have chosen the poly-(lactide-glycolide)-acrylic acid PLGA − AA hydrogel, where AA-groups are believed to play the role of quasi-mobile nodes in the formation of a network. One output of the model is the change of energy density during tensile deformation which is then used to calculate the stress–strain relationship.

Constraint effect on the slow crack growth in polyethylene

Purpose – From the practical point of view, most relevant damage to high density polyethylene (HDPE) structures is caused by slow crack growth. Therefore, detailed information about this type of damage is necessary. Experimental results transfer from specimens to real structure can be influenced by structure geometry (constraint). Therefore, the purpose of this paper is to investigate and discuss the effect of the constraint and relation between crack mouth opening displacement (CMOD) and crack length.Design/methodology/approach – The constraint effect is mainly effect of the structure geometry and can be quantified by T‐stress. Two different test specimens with different constraint level (T‐stress) were prepared: single edge notched specimen and modified single edge notch (SEN) specimen. The crack mouth opening displacement, crack tip opening displacement and crack length was measured.Findings – The main conclusions of this work can be summarized as: the slow crack growth rate in HDPE materials correspon...

Simulation of Inelastic Stress - Strain Response of Nanocomposites by a Network Model

This paper describes the viscoelastic properties of network model. In the first approximation, nanocomposite was modeled as a 3D tetrafunctional network considering entanglements to act as the physical x-links. Nano-sized non-deformable domains of defined shape and size were introduced into the network. The chains in the vicinity of the inclusions were considered immobilized. Hence, the semicrystalline polymer was considered a three-phase system containing flexible matrix bulk phase, immobilized chains near the inclusion surface and rigid crystalline domains. The crystallites were characterized by their Youngs modulus and their traction properties were calculated using the Hookes law. Unlike the model, the real polymer has viscoelastic deformation properties. The components which could cause viscoelastic properties were introduced and their impact on viscoelastic properties of whole network was investigated. The components were for example the reptation motion of chain in entanglements or chain, whose motion was retarded by impact of surroundings. The model enabled to investigate the influence of each component, as well as the influence of distribution of each component. The types of nods, whose influence was investigated in this contribution, were fast knot, free entanglement, one-way entanglement and energy barrier.

The Effect of Network Solvation on the Viscoelastic Response of Polymer Hydrogels

The majority of investigations consider the deformation response of hydrogels, fully controlled by the deformation behavior of their polymer network, neglecting the contribution caused by the presence of water. Here, we use molecular dynamics simulation in an attempt to include the effect of physically bound water via polymer chain solvation on the viscoelastic response of hydrogels. Our model allows us to control the solvation of chains as an independent variable. The solvation of the chain is independent of other factors, mainly the effect (pH) which interferes significantly in experiments. The solvation of hydrophilic chains was controlled by setting a partial charge on the chains and quantified by the Bjerrum length (BL). The BL was calculated from the partial electric charge of the solvent and macromolecular network. When the BL is short, the repulsive Van der Waals interactions are predominant in the vicinity of macromolecules and solvation is not observed. For a long BL, the water molecules in the solvation zone of network are in the same range as attractive intermolecular forces and the solvation occurs. The model also allows the consideration of molecules of water attached to two chains simultaneously, forming a temporary bridging. By elucidating the relations between solvation of the network and structural changes during the network deformation, one may predict the viscoelastic properties of hydrogels knowing the molecular structure of its polymer chains.

Selection of Points Inside Cutoff Radius by Scanning All Points Sorted in Memory

A method for selection inside-cutoff points from a cloud of finite number of points was presented. The cutoff points are in less or equal distance from reference object than a given radius. This radius is user-defined input value. The proposed algorithm was inspired by a function of ribosome. Ribosome in living cells translates linear structure of ribonucleic acid to the complex structure of protein. In the virtual model of ribosome, similar functions were programmed. The linear structure of messenger-RNA was replaced by RAM. Programme immitated slider traversing the RAM. Inside the slider, there was linked list or binary search tree acting similarly like translation RNA in ribosome. The method applied to the searching the cutoff-points showed acceleration in comparison to classic methods.

Molecular Dynamics Simulation of Single Chain in the Vicinity of Nanoparticle

Molecular simulation of single chain in the vicinity of nanoparticle in comparison with pure system is presented. According to the Rouse theory, chains were considered as a sequence of beads connected together by harmonic springs. The motion of atoms was supported by thermal energy and retarded by the resistance of surrounding. New atom position, in given time, was determined by the Smoluchowski equation, that consists of two terms: first one includes the influence of the inter-atomic collisions, the sterical obstacles and the strong intermolecular interactions in friction coefficient, second one express the energy field aggregated from potentials of all atoms. Sinusoidal shear stress was applied to the chain. The output of the model was energy as a function of time. The energy course was also sinusoidal but shifted according to the deformation. The amplitudes and phase shifts were analyzed for the chains under different conditions .The chains were subjected to the model first as the standalone objects. Then, barrier was defined and chains placed in the vicinity of it. The barrier acted as a volume excluded hindrance. This type of chain molecular dynamics could be used as a stand-alone model or it could be suitable component for complex models, for example network model of polymer nanocomposite.