The regeneration of the nervous system is a challenging task. Currently, regenerative medicine ap... more The regeneration of the nervous system is a challenging task. Currently, regenerative medicine approaches that exploit nature-inspired cues are being studied and hold great promise. The possibility to use protein-based matrices functionalized with small oligo- and monosaccharides is of interest since these can be finely tuned to better mimic the native environment. Collagen has been selected as a promising material that has the potential to be further tailored to incorporate carbohydrates in order to drive cell behavior towards neuroregeneration. Indeed, the grafting of carbohydrates to collagen 2D matrices is proved to enhance its biological significance. In the present study, collagen 2D matrices were grafted with different carbohydrate epitopes, and their potential to drive F-11 neuroblastoma cells towards neuronal differentiation was evaluated. Collagen functionalized with α-glucosides was able to differentiate neuroblastoma cells into functional neurons, while sialyl α-(2→6)-ga...
The osmotic pressure of chondroitin sulfate glycosaminoglycans (CS-GAGs) in a simulated physiolog... more The osmotic pressure of chondroitin sulfate glycosaminoglycans (CS-GAGs) in a simulated physiological environment of articular cartilage is thoroughly examined in silico using full atomistic models. The effects of chemical and physical properties were investigated to elucidate the molecular origins of cartilage biomechanical behavior providing single-atomistic resolution analyses which would not be attainable with in vivo or in in vitro techniques. CS-GAG chains exhibit plastic deformation behavior under compressive load in the extracellular matrix (ECM) and osmotic pressure is the main contributor in balancing external pressures. This study focuses on quantitatively expressing this contribution. Molecular dynamics was used to imitate the physiological environment experienced by GAGs inside articular cartilage by simulating a semipermeable membrane acting on the full atomistic chains during compression. To this end, a variety of validation techniques, pre-simulation tasks, and compa...
The International Journal of Artificial Organs, 2006
Extracorporeal endotoxin removal by means of the Toraymyxin device is based on the ability of pol... more Extracorporeal endotoxin removal by means of the Toraymyxin device is based on the ability of polymyxin B to bind endotoxins with a high specificity. The endotoxins/polymyxin molecular interactions were computationally analyzed in a parallel work (Part I). In this paper we investigate with a multi-scale approach the phenomena involving blood and plasma fluid dynamics inside the device. The macro- and mesoscale phenomena were studied by means of 3D models using computational fluid dynamics. The flow behavior in the sorbent material was focused, modeling the sorbent as a homogeneous porous medium at the macroscale level, or accounting for the realistic geometry of its knitted fibers at the mesoscale level. A microscale model was then developed to analyze the behavior of endotoxin molecules subjected to the competition of flow drag and molecular attraction by fibergrafted polymyxin B. The macroscale results showed that a very regular flow field develops in the sorbent, furthermore supp...
Osteogenesis imperfecta (abbreviated as OI) is a genetic disorder in collagen characterized by me... more Osteogenesis imperfecta (abbreviated as OI) is a genetic disorder in collagen characterized by mechanically weakened tendon, fragile bones, skeletal deformities and in severe cases prenatal death. Even though many studies have attempted to associate specific mutation types with phenotypic severity, the molecular and mesoscale mechanisms by which a single point mutation influences the mechanical behavior of tissues at multiple length-scales remain unknown. Here we review results of a hierarchy of full atomistic and mesoscale simulations that demonstrated that OI mutations severely compromise the mechanical properties of collagenous tissues at multiple scales, from single molecules to collagen fibrils. Notably, mutations that lead to the most severe OI phenotype correlate with the strongest effects, leading to weakened intermolecular adhesion, increased intermolecular spacing, reduced stiffness, as well as a reduced failure strength of collagen fibrils (Gautieri et al., Biophys. J., 2...
Theoretical prediction of the mechanical properties of soft tissues usually relies on a top-down ... more Theoretical prediction of the mechanical properties of soft tissues usually relies on a top-down approach; that is analysis is gradually refined to observe smaller structures and properties until technical limits are reached. Computer-Assisted Molecular Modeling (CAMM) allows for the reversal of this approach and the performance of bottom-up modeling instead. The wealth of available sequences and structures provides an enormous database for computational efforts to predict structures, simulate docking and folding processes, simulate molecular interactions, and understand them in quantitative energetic terms. Tendons and ligaments can be considered an ideal arena due to their well defined and highly organized architecture which involves not only the main structural constituent, the collagen molecule, but also other important molecular "actors" such as proteoglycans and glycosaminoglycans. In this ideal arena each structure is well organized and recognizable, and using the m...
One of the merging methods to produce tissue-engineered vascular substitutes is to process scaffo... more One of the merging methods to produce tissue-engineered vascular substitutes is to process scaffolds to direct the regeneration of vascular tissues. Collagen, as one of the main protein in the vascular extracellular matrix, is one of biopolymers that exhibits a major potential for scaffold technology. However, gels made from reconstituted collagen generally exhibit poor mechanical properties and limited manipulability. Therefore, adding a reinforcement to the scaffold to make the structure resist to the physiological constraints applied during the regeneration represents a valid alternative. Silk fibroin is an interesting reinforcing candidate being a mechanically strong natural fibre, susceptible to proteolytic degradation in vivo and showing acceptable biological performances. Therefore, the aim of this study was to develop a model of a composite scaffold obtained by controlling the filament geometry winding of silk fibroin in the collagen gel. A finite element model taking into account the orthotropic elasticity of arteries has been combined with classic laminate theory applied to the filament winding of a tubular vessel. The design of the small structure susceptible to scaffold the vascular tissue regeneration was optimised by mean of an evolutive algorithm with the imperative to mimic the experimentally measured mechanical properties (compliance) of a native artery.
Collagen is the most used naturally occurring scaffold material. It’s a structural protein ubiqui... more Collagen is the most used naturally occurring scaffold material. It’s a structural protein ubiquitous among mammalian. The ability of collagen type I to host different cell phenotype in vitro and its low antigenecity in vivo are well known. However, the principal drawback of collagenbased materials consists in their low mechanical properties. For vascular tissue engineering this represents a major limit, as the aim is to mimic the structure of a native vessel, which is known to be resistant and viscoelastic. Moreover, vascular cells are known to be susceptible in vivo to reorganize the matrix in which they proliferate. Therefore, the aim of this project is to study the micro structural organization of collagen-based scaffolds, and to assess the interactions between collagen and smooth muscle cells during regeneration. This knowledge will then allow the development of appropriate strategies to tailor the microstructure of the scaffold and its properties. Smooth muscle cells (SMCs) we...
Journal of Applied Biomaterials and Biomechanics, 2011
The present article reviews on different research lines, namely: drug and gene delivery, surface ... more The present article reviews on different research lines, namely: drug and gene delivery, surface modification/modeling, design of advanced materials (shape memory polymers and biodegradable stents), presently developed at Politecnico di Milano, Italy. For gene delivery, non-viral polycationic-branched polyethylenimine (b-PEI) polyplexes are coated with pectin, an anionic polysaccharide, to enhance the polyplex stability and decrease b-PEI cytotoxicity. Perfluorinated materials, specifically perfluoroether, and perfluoro-polyether fluids are proposed as ultrasound contrast agents and smart agents for drug delivery. Non-fouling, self-assembled PEG-based monolayers are developed on titanium surfaces with the aim of drastically reducing cariogenic bacteria adhesion on dental implants. Femtosecond laser microfabrication is used for selectively and spatially tuning the wettability of polymeric biomaterials and the effects of femtosecond laser ablation on the surface properties of polymethylmethacrylate are studied. Innovative functionally graded Alumina-Ti coatings for wear resistant articulating surfaces are deposited with PLD and characterized by means of a combined experimental and computational approach. Protein adsorption on biomaterials surfaces with an unlike wettability and surface-modification induced by pre-adsorbed proteins are studied by atomistic computer simulations. A study was performed on the fabrication of porous Shape Memory Polymeric structures and on the assessment of their potential application in minimally invasive surgical procedures. A model of magnesium (alloys) degradation, in a finite element framework analysis, and a bottom-up multiscale analysis for modeling the degradation mechanism of PLA matrices was developed, with the aim of providing valuable tools for the design of bioresorbable stents.
The removal of blood endotoxins with the Toraymyxin extracorporeal sorption device exploits the c... more The removal of blood endotoxins with the Toraymyxin extracorporeal sorption device exploits the capability of immobilized polymyxin B (PMB) to bind endotoxins stably with a high specificity. Although adsorption is a molecular-scale mechanism, it involves hydrodynamic phenomena in the whole range from the macroscopic down to the supramolecular scales. In this paper we summarize our experience with a computational, multiscale investigation of this device's hydrodynamic functionality. 3D computational fluid dynamics models were developed for the upper-scale studies. The flow behavior in the sorbent material was either modeled as a homogeneous Darcy's flow (macroscale study), or described as the flow through realistic geometrical models of its knitted fibers (mesoscale study). In the microscale study, simplified 2D models were used to track the motion of modeled endotoxin particles subjected to the competition of flow drag and molecular attraction by the fiber-grafted PMB. The results at each scale level supplied worst-case input data for the subsequent study. The macroscale results supplied the peak velocity of the flow field that develops in the sorbent. This was used in the mesoscale analysis, yielding a realistic range for the shear stresses in the fluid next to the fiber surface. With wall shear stresses in this range, endotoxin particle tracking was studied both in the vicinity of a single immobilized PMB molecule, and in the presence of a layer of PMB molecules evenly distributed at the fiber surface. Results showed that the capability to seize endotoxin molecules extends at least at a distance of 10-20 nm from the surface, which is one order of magnitude greater than the stable intermolecular bond characteristic distance. We conclude that a multiscale approach has the power to provide a comprehensive understanding, shedding light both upon the physics involved at each scale level and the mutual interactions of phenomena occurring at different scales.
One of the most promising applications of hydrolytically degrading biomaterials is their use as d... more One of the most promising applications of hydrolytically degrading biomaterials is their use as drug release carriers. These uses, however, require that the degradation and diffusion of drug are reliably predicted, which is complex to achieve through present experimental methods. Atomistic modeling can help in the knowledge-based design of degrading biomaterials with tuned drug delivery properties, giving insights on the small molecules diffusivity at intermediate states of the degradation process. We present here an atomistic-based approach to investigate the diffusion of water (through which hydrolytic degradation occurs) in degrading bulk models of poly(lactic acid) or PLA. We determine the water diffusion coefficient for different swelling states of the polymeric matrix (from almost dry to pure water) and for different degrees of degradation. We show that water diffusivity is highly influenced by the swelling degree, while little or not influenced by the degradation state. This approach, giving water diffusivity for different states of the matrix, can be combined with diffusion-reaction analytical methods in order to predict the degradation path on longer time scales. Furthermore, atomistic approach can be used to investigate diffusion of other relevant small molecules, eventually leading to the a priori knowledge of degradable biomaterials transport properties, helping the design of the drug delivery systems.
The regeneration of the nervous system is a challenging task. Currently, regenerative medicine ap... more The regeneration of the nervous system is a challenging task. Currently, regenerative medicine approaches that exploit nature-inspired cues are being studied and hold great promise. The possibility to use protein-based matrices functionalized with small oligo- and monosaccharides is of interest since these can be finely tuned to better mimic the native environment. Collagen has been selected as a promising material that has the potential to be further tailored to incorporate carbohydrates in order to drive cell behavior towards neuroregeneration. Indeed, the grafting of carbohydrates to collagen 2D matrices is proved to enhance its biological significance. In the present study, collagen 2D matrices were grafted with different carbohydrate epitopes, and their potential to drive F-11 neuroblastoma cells towards neuronal differentiation was evaluated. Collagen functionalized with α-glucosides was able to differentiate neuroblastoma cells into functional neurons, while sialyl α-(2→6)-ga...
The osmotic pressure of chondroitin sulfate glycosaminoglycans (CS-GAGs) in a simulated physiolog... more The osmotic pressure of chondroitin sulfate glycosaminoglycans (CS-GAGs) in a simulated physiological environment of articular cartilage is thoroughly examined in silico using full atomistic models. The effects of chemical and physical properties were investigated to elucidate the molecular origins of cartilage biomechanical behavior providing single-atomistic resolution analyses which would not be attainable with in vivo or in in vitro techniques. CS-GAG chains exhibit plastic deformation behavior under compressive load in the extracellular matrix (ECM) and osmotic pressure is the main contributor in balancing external pressures. This study focuses on quantitatively expressing this contribution. Molecular dynamics was used to imitate the physiological environment experienced by GAGs inside articular cartilage by simulating a semipermeable membrane acting on the full atomistic chains during compression. To this end, a variety of validation techniques, pre-simulation tasks, and compa...
The International Journal of Artificial Organs, 2006
Extracorporeal endotoxin removal by means of the Toraymyxin device is based on the ability of pol... more Extracorporeal endotoxin removal by means of the Toraymyxin device is based on the ability of polymyxin B to bind endotoxins with a high specificity. The endotoxins/polymyxin molecular interactions were computationally analyzed in a parallel work (Part I). In this paper we investigate with a multi-scale approach the phenomena involving blood and plasma fluid dynamics inside the device. The macro- and mesoscale phenomena were studied by means of 3D models using computational fluid dynamics. The flow behavior in the sorbent material was focused, modeling the sorbent as a homogeneous porous medium at the macroscale level, or accounting for the realistic geometry of its knitted fibers at the mesoscale level. A microscale model was then developed to analyze the behavior of endotoxin molecules subjected to the competition of flow drag and molecular attraction by fibergrafted polymyxin B. The macroscale results showed that a very regular flow field develops in the sorbent, furthermore supp...
Osteogenesis imperfecta (abbreviated as OI) is a genetic disorder in collagen characterized by me... more Osteogenesis imperfecta (abbreviated as OI) is a genetic disorder in collagen characterized by mechanically weakened tendon, fragile bones, skeletal deformities and in severe cases prenatal death. Even though many studies have attempted to associate specific mutation types with phenotypic severity, the molecular and mesoscale mechanisms by which a single point mutation influences the mechanical behavior of tissues at multiple length-scales remain unknown. Here we review results of a hierarchy of full atomistic and mesoscale simulations that demonstrated that OI mutations severely compromise the mechanical properties of collagenous tissues at multiple scales, from single molecules to collagen fibrils. Notably, mutations that lead to the most severe OI phenotype correlate with the strongest effects, leading to weakened intermolecular adhesion, increased intermolecular spacing, reduced stiffness, as well as a reduced failure strength of collagen fibrils (Gautieri et al., Biophys. J., 2...
Theoretical prediction of the mechanical properties of soft tissues usually relies on a top-down ... more Theoretical prediction of the mechanical properties of soft tissues usually relies on a top-down approach; that is analysis is gradually refined to observe smaller structures and properties until technical limits are reached. Computer-Assisted Molecular Modeling (CAMM) allows for the reversal of this approach and the performance of bottom-up modeling instead. The wealth of available sequences and structures provides an enormous database for computational efforts to predict structures, simulate docking and folding processes, simulate molecular interactions, and understand them in quantitative energetic terms. Tendons and ligaments can be considered an ideal arena due to their well defined and highly organized architecture which involves not only the main structural constituent, the collagen molecule, but also other important molecular "actors" such as proteoglycans and glycosaminoglycans. In this ideal arena each structure is well organized and recognizable, and using the m...
One of the merging methods to produce tissue-engineered vascular substitutes is to process scaffo... more One of the merging methods to produce tissue-engineered vascular substitutes is to process scaffolds to direct the regeneration of vascular tissues. Collagen, as one of the main protein in the vascular extracellular matrix, is one of biopolymers that exhibits a major potential for scaffold technology. However, gels made from reconstituted collagen generally exhibit poor mechanical properties and limited manipulability. Therefore, adding a reinforcement to the scaffold to make the structure resist to the physiological constraints applied during the regeneration represents a valid alternative. Silk fibroin is an interesting reinforcing candidate being a mechanically strong natural fibre, susceptible to proteolytic degradation in vivo and showing acceptable biological performances. Therefore, the aim of this study was to develop a model of a composite scaffold obtained by controlling the filament geometry winding of silk fibroin in the collagen gel. A finite element model taking into account the orthotropic elasticity of arteries has been combined with classic laminate theory applied to the filament winding of a tubular vessel. The design of the small structure susceptible to scaffold the vascular tissue regeneration was optimised by mean of an evolutive algorithm with the imperative to mimic the experimentally measured mechanical properties (compliance) of a native artery.
Collagen is the most used naturally occurring scaffold material. It’s a structural protein ubiqui... more Collagen is the most used naturally occurring scaffold material. It’s a structural protein ubiquitous among mammalian. The ability of collagen type I to host different cell phenotype in vitro and its low antigenecity in vivo are well known. However, the principal drawback of collagenbased materials consists in their low mechanical properties. For vascular tissue engineering this represents a major limit, as the aim is to mimic the structure of a native vessel, which is known to be resistant and viscoelastic. Moreover, vascular cells are known to be susceptible in vivo to reorganize the matrix in which they proliferate. Therefore, the aim of this project is to study the micro structural organization of collagen-based scaffolds, and to assess the interactions between collagen and smooth muscle cells during regeneration. This knowledge will then allow the development of appropriate strategies to tailor the microstructure of the scaffold and its properties. Smooth muscle cells (SMCs) we...
Journal of Applied Biomaterials and Biomechanics, 2011
The present article reviews on different research lines, namely: drug and gene delivery, surface ... more The present article reviews on different research lines, namely: drug and gene delivery, surface modification/modeling, design of advanced materials (shape memory polymers and biodegradable stents), presently developed at Politecnico di Milano, Italy. For gene delivery, non-viral polycationic-branched polyethylenimine (b-PEI) polyplexes are coated with pectin, an anionic polysaccharide, to enhance the polyplex stability and decrease b-PEI cytotoxicity. Perfluorinated materials, specifically perfluoroether, and perfluoro-polyether fluids are proposed as ultrasound contrast agents and smart agents for drug delivery. Non-fouling, self-assembled PEG-based monolayers are developed on titanium surfaces with the aim of drastically reducing cariogenic bacteria adhesion on dental implants. Femtosecond laser microfabrication is used for selectively and spatially tuning the wettability of polymeric biomaterials and the effects of femtosecond laser ablation on the surface properties of polymethylmethacrylate are studied. Innovative functionally graded Alumina-Ti coatings for wear resistant articulating surfaces are deposited with PLD and characterized by means of a combined experimental and computational approach. Protein adsorption on biomaterials surfaces with an unlike wettability and surface-modification induced by pre-adsorbed proteins are studied by atomistic computer simulations. A study was performed on the fabrication of porous Shape Memory Polymeric structures and on the assessment of their potential application in minimally invasive surgical procedures. A model of magnesium (alloys) degradation, in a finite element framework analysis, and a bottom-up multiscale analysis for modeling the degradation mechanism of PLA matrices was developed, with the aim of providing valuable tools for the design of bioresorbable stents.
The removal of blood endotoxins with the Toraymyxin extracorporeal sorption device exploits the c... more The removal of blood endotoxins with the Toraymyxin extracorporeal sorption device exploits the capability of immobilized polymyxin B (PMB) to bind endotoxins stably with a high specificity. Although adsorption is a molecular-scale mechanism, it involves hydrodynamic phenomena in the whole range from the macroscopic down to the supramolecular scales. In this paper we summarize our experience with a computational, multiscale investigation of this device's hydrodynamic functionality. 3D computational fluid dynamics models were developed for the upper-scale studies. The flow behavior in the sorbent material was either modeled as a homogeneous Darcy's flow (macroscale study), or described as the flow through realistic geometrical models of its knitted fibers (mesoscale study). In the microscale study, simplified 2D models were used to track the motion of modeled endotoxin particles subjected to the competition of flow drag and molecular attraction by the fiber-grafted PMB. The results at each scale level supplied worst-case input data for the subsequent study. The macroscale results supplied the peak velocity of the flow field that develops in the sorbent. This was used in the mesoscale analysis, yielding a realistic range for the shear stresses in the fluid next to the fiber surface. With wall shear stresses in this range, endotoxin particle tracking was studied both in the vicinity of a single immobilized PMB molecule, and in the presence of a layer of PMB molecules evenly distributed at the fiber surface. Results showed that the capability to seize endotoxin molecules extends at least at a distance of 10-20 nm from the surface, which is one order of magnitude greater than the stable intermolecular bond characteristic distance. We conclude that a multiscale approach has the power to provide a comprehensive understanding, shedding light both upon the physics involved at each scale level and the mutual interactions of phenomena occurring at different scales.
One of the most promising applications of hydrolytically degrading biomaterials is their use as d... more One of the most promising applications of hydrolytically degrading biomaterials is their use as drug release carriers. These uses, however, require that the degradation and diffusion of drug are reliably predicted, which is complex to achieve through present experimental methods. Atomistic modeling can help in the knowledge-based design of degrading biomaterials with tuned drug delivery properties, giving insights on the small molecules diffusivity at intermediate states of the degradation process. We present here an atomistic-based approach to investigate the diffusion of water (through which hydrolytic degradation occurs) in degrading bulk models of poly(lactic acid) or PLA. We determine the water diffusion coefficient for different swelling states of the polymeric matrix (from almost dry to pure water) and for different degrees of degradation. We show that water diffusivity is highly influenced by the swelling degree, while little or not influenced by the degradation state. This approach, giving water diffusivity for different states of the matrix, can be combined with diffusion-reaction analytical methods in order to predict the degradation path on longer time scales. Furthermore, atomistic approach can be used to investigate diffusion of other relevant small molecules, eventually leading to the a priori knowledge of degradable biomaterials transport properties, helping the design of the drug delivery systems.
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Papers by Simone Vesentini