... and improper torsion angle, respectively, with the subscript zero representing the equilibriu... more ... and improper torsion angle, respectively, with the subscript zero representing the equilibrium posi-tions ... mechanisms), this translates into the properties of molecules at large-strain, a phenomenon ... Elastic Network Model (ENM) [78], Gaussian Network Model (GNM) [79] and Go ...
Alpha-helix based protein networks as they appear in intermediate filaments in the cell's cyt... more Alpha-helix based protein networks as they appear in intermediate filaments in the cell's cytoskeleton and the nuclear membrane robustly withstand large deformation of up to several hundred percent strain, despite the presence of structural imperfections or flaws. This performance is not achieved by most synthetic materials, which typically fail at much smaller deformation and show a great sensitivity to the existence of structural flaws. Here we report a series of molecular dynamics simulations with a simple coarse-grained multi-scale model of alpha-helical protein domains, explaining the structural and mechanistic basis for this observed behavior. We find that the characteristic properties of alpha-helix based protein networks are due to the particular nanomechanical properties of their protein constituents, enabling the formation of large dissipative yield regions around structural flaws, effectively protecting the protein network against catastrophic failure. We show that th...
Graphene is a truly two-dimensional atomic crystal with exceptional electronic and mechanical pro... more Graphene is a truly two-dimensional atomic crystal with exceptional electronic and mechanical properties. Whereas conventional bulk and thin film materials have been studied extensively, the key mechanical properties of graphene, such as tearing and cracking, remain unknown, partly due to its two-dimensional nature and ultimate singleatom-layer thickness, which result in the breakdown of conventional material models. By combining first-principles ReaxFF molecular dynamics and experimental studies, a bottomup investigation of the tearing of graphene sheets from adhesive substrates is reported, including the observation of the formation of tapered graphene nanoribbons. Through a careful analysis of the underlying molecular rupture mechanisms, it is shown that the resulting nanoribbon geometry is controlled by both the graphene-substrate adhesion energy and by the number of torn graphene layers. By considering graphene as a model material for a broader class of two-dimensional atomic crystals, these results provide fundamental insights into the tearing and cracking mechanisms of highly confined nanomaterials.
At low temperatures silicon is a brittle material that shatters catastrophically, whereas at elev... more At low temperatures silicon is a brittle material that shatters catastrophically, whereas at elevated temperatures, the behavior of silicon changes drastically over a narrow temperature range and suddenly becomes ductile. This brittle-to-ductile transition has been observed in experimental studies, yet its fundamental mechanisms remain unknown. Here we report an atomistic-level study of a fundamental event in this transition, the change from brittle cleavage fracture to dislocation emission at crack tips, using the first principles based reactive force field. By solely raising the temperature, we observe an abrupt change from brittle cracking to dislocation emission from a crack within a %10 K temperature interval.
Theoretical and molecular dynamics analyses of a confined crack under mode II shear loading in a ... more Theoretical and molecular dynamics analyses of a confined crack under mode II shear loading in a simple thin strip geometry reveals that two universal, intrinsic material length scales control the mechanism of plastic deformation in single nanocrystals under a geometric confinement. These two length scales control the occurrence of complete dislocation, partial dislocation, and no dislocation nucleations from defects. Our results explain the earlier experimental and computational observations that have shown a change in the deformation mechanism under a geometric confinement, which is illustrated here in a specific, simple geometrical setup that reveals the governing physical mechanisms of plasticity under an extreme geometric confinement. We illustrate the significance of our findings in an analysis of the size dependence of the flow stress of a bioinspired nanocomposite.
A universal design paradigm in biology is the use of hierarchies, which is evident in the structu... more A universal design paradigm in biology is the use of hierarchies, which is evident in the structure of proteins, cells, tissues, and organisms, as well as outside the material realm in the design of signaling networks in complex organs such as the brain. A fascinating example of a biological structure is that of diatoms, a microscopic mineralized algae that is mainly composed of amorphous silica, which features a hierarchical structure that ranges from the nano-to the macroscale. Here, we use the porous structure found at submicron length scales in diatom algae as a basis to study a bioinspired nanoporous material implemented in crystalline silica. We consider the mechanical performance of two nanoscale levels of hierarchy, studying an array of thin-walled foil silica structures and a hierarchical arrangement of foil elements into a porous silica mesh structure. By comparing their elastic, plastic, and failure mechanisms under tensile deformation, we elucidate the impact of hierarchies and the wall width of constituting silica foils on the mechanical properties, by carrying out a series of large-scale molecular dynamics (MD) simulations with the first principles based reactive force field ReaxFF. We find that by controlling the wall width and by increasing the level of hierarchy of the nanostructure from a foil to a mesh, it is possible to significantly enhance the mechanical response of the material, creating a highly deformable, strong, and extremely tough material that can be stretched in excess of 100 pct strain, in stark contrast to the characteristic brittle performance of bulk silica. We find that concurrent mechanisms of shearing and crack arrest lead to an enhanced toughness and are enabled through the hierarchical assembly of foil elements into a mesh structure, which could not be achieved in foil structures alone. Our results demonstrate that including higher levels of hierarchy are beneficial in improving the mechanical properties and deformability of intrinsically brittle materials. The findings reported here provide insight into general material design approaches that may enable us to transform a brittle material such as silicon or silica into a ductile, yet strong and tough material, solely through alterations of its structural arrangement at the nanoscale.
We model a single crystal of silicon approaching dimensions of 20 nm × 20 nm × 10 nm with up to 2... more We model a single crystal of silicon approaching dimensions of 20 nm × 20 nm × 10 nm with up to 200,000 atoms based on the ReaxFF first principles based reactive force field, applied here to examine the influence of crack tip heterogeneities on the nucleation of dislocations from crack tips as the temperature is increased well beyond 1000 K. Our study aims at generating insight into mechanisms of the brittle-toductile transition (BDT) observed in silicon, which is known to change the behavior of silicon crystals from predominantly brittle at low temperatures to ductile at higher temperatures, likely involving a competition between brittle bond-breaking and emission of dislocations. We first examine the crystallographic orientations most widely known to exhibit fracture, for example failure on the {1 1 1} and {1 1 0} planes. We find that even at very high temperatures considered here (around 1500 K), the material behaved in a completely brittle manner for systems with cracks oriented in the {1 1 1} and {1 1 0} planes. In contrast, when the crack plane is changed to the {1 0 0} orientation, the formation of complete dislocation loops is observed. The results reported in our paper is the first direct observation of dislocation loops in silicon driven by an increase in the temperature, and extends earlier studies that were focused solely on extremely thin quasi-two-dimensional models. We demonstrate here that the formation of these loops can be linked to the geometrical ledges at the crack tip with favorable orientations for slip on the {1 1 1} planes. The detailed mechanisms leading to the nucleation of dislocations involve changes at the crack tip with bond rotations and formation of ledges, and we find that the emergence of dislocations causes the crack to arrest, but re-initiation takes place and no conclusive nucleation of dislocations and complete arrest of the crack is observed. The thickness effect is discussed together with other sources for formation of ledges along the crack front. Our findings provide important insight towards the development of models for the brittle-ductile-transition in silicon and potentially other materials, and emphasize on the significance of thickness effects in simulations of fracture in crystal slabs.
Journal of Computational and Theoretical Nanoscience, 2010
The recent discovery of single graphene sheets and the remarkable technologies envisioned for gra... more The recent discovery of single graphene sheets and the remarkable technologies envisioned for graphene-based materials necessitate the ability to assemble and reproduce nano-precise graphene structures. Here we demonstrate an approach to create atomically precise single graphene structures by applying tensile load to single sheets of graphene that feature specific patterns of vacancies. We report a computational nanoengineering approach that utilizes the first principles based reactive force field potential (ReaxFF), applied here to simulate the fracture mechanics of up to 40,000 fully reactive atoms. We find that the direction and dynamical behavior of graphene fracture can be controlled by the presence of atomistic defects in the form of atomic vacancies placed throughout the sheet. We find that these vacancies produce distinct effects on the resulting fracture surface geometries, defined by the specific patterns in which they occur throughout the 2D structure. For instance, we are able to cut graphene sheets along controlled zigzag patterns on the nanoscale using specific arrangements of vacancies. These findings suggest novel possibilities aimed at cutting and producing atomically precise graphene structures, enabling advances in graphene nanotechnology. The study reported here is the first to apply ReaxFF to model fracture of graphene sheets.
Journal of Algorithms & Computational Technology, 2008
We report a novel multi-paradigm multi-scale approach based on a combination of the first princip... more We report a novel multi-paradigm multi-scale approach based on a combination of the first principles ReaxFF force field with an empirical Tersoff potential. Our hybrid multi-scale simulation model is computationally efficient and capable of treating thousands of atoms with QM accuracy, extending our ability to simulate the dynamical behavior of a wider range of chemically complex materials such as silicon, silica and metal-organic compounds. It is implemented in the Python based Computational Materials Design Facility (CMDF). We exemplify our method in a study focused on a systematic comparison of the fracture dynamics in silicon under mode II shear versus mode I tensile loading. We find that the mode II crack tends to branch at an angle of approximately 45 degrees once the crack speed approaches 38% of the Rayleigh-wave speed. In contrast, the mode I crack continuously propagates in the direction of the initial crack, and only makes a slight change of direction towards 10 degrees once fracture instabilities occur. Our results reveal fundamental differences of fracture dynamics under mode I versus mode II loading.
International Journal for Multiscale Computational Engineering, 2007
ABSTRACT Prediction of the deformation behavior of metals in the presence of environmentally embr... more ABSTRACT Prediction of the deformation behavior of metals in the presence of environmentally embrittling species like water or hydrogen, or under presence of organic reactive chemicals, remains a critical challenge in materials modeling. Here we propose a ...
Graphene features unique electronic, thermal, and mechanical properties, and the flexibility and ... more Graphene features unique electronic, thermal, and mechanical properties, and the flexibility and strong attraction between graphene layers promotes the formation of self-folded nanostructures. Here we study the self-folding of mono-and multilayer graphene sheets, ...
... and improper torsion angle, respectively, with the subscript zero representing the equilibriu... more ... and improper torsion angle, respectively, with the subscript zero representing the equilibrium posi-tions ... mechanisms), this translates into the properties of molecules at large-strain, a phenomenon ... Elastic Network Model (ENM) [78], Gaussian Network Model (GNM) [79] and Go ...
Alpha-helix based protein networks as they appear in intermediate filaments in the cell's cyt... more Alpha-helix based protein networks as they appear in intermediate filaments in the cell's cytoskeleton and the nuclear membrane robustly withstand large deformation of up to several hundred percent strain, despite the presence of structural imperfections or flaws. This performance is not achieved by most synthetic materials, which typically fail at much smaller deformation and show a great sensitivity to the existence of structural flaws. Here we report a series of molecular dynamics simulations with a simple coarse-grained multi-scale model of alpha-helical protein domains, explaining the structural and mechanistic basis for this observed behavior. We find that the characteristic properties of alpha-helix based protein networks are due to the particular nanomechanical properties of their protein constituents, enabling the formation of large dissipative yield regions around structural flaws, effectively protecting the protein network against catastrophic failure. We show that th...
Graphene is a truly two-dimensional atomic crystal with exceptional electronic and mechanical pro... more Graphene is a truly two-dimensional atomic crystal with exceptional electronic and mechanical properties. Whereas conventional bulk and thin film materials have been studied extensively, the key mechanical properties of graphene, such as tearing and cracking, remain unknown, partly due to its two-dimensional nature and ultimate singleatom-layer thickness, which result in the breakdown of conventional material models. By combining first-principles ReaxFF molecular dynamics and experimental studies, a bottomup investigation of the tearing of graphene sheets from adhesive substrates is reported, including the observation of the formation of tapered graphene nanoribbons. Through a careful analysis of the underlying molecular rupture mechanisms, it is shown that the resulting nanoribbon geometry is controlled by both the graphene-substrate adhesion energy and by the number of torn graphene layers. By considering graphene as a model material for a broader class of two-dimensional atomic crystals, these results provide fundamental insights into the tearing and cracking mechanisms of highly confined nanomaterials.
At low temperatures silicon is a brittle material that shatters catastrophically, whereas at elev... more At low temperatures silicon is a brittle material that shatters catastrophically, whereas at elevated temperatures, the behavior of silicon changes drastically over a narrow temperature range and suddenly becomes ductile. This brittle-to-ductile transition has been observed in experimental studies, yet its fundamental mechanisms remain unknown. Here we report an atomistic-level study of a fundamental event in this transition, the change from brittle cleavage fracture to dislocation emission at crack tips, using the first principles based reactive force field. By solely raising the temperature, we observe an abrupt change from brittle cracking to dislocation emission from a crack within a %10 K temperature interval.
Theoretical and molecular dynamics analyses of a confined crack under mode II shear loading in a ... more Theoretical and molecular dynamics analyses of a confined crack under mode II shear loading in a simple thin strip geometry reveals that two universal, intrinsic material length scales control the mechanism of plastic deformation in single nanocrystals under a geometric confinement. These two length scales control the occurrence of complete dislocation, partial dislocation, and no dislocation nucleations from defects. Our results explain the earlier experimental and computational observations that have shown a change in the deformation mechanism under a geometric confinement, which is illustrated here in a specific, simple geometrical setup that reveals the governing physical mechanisms of plasticity under an extreme geometric confinement. We illustrate the significance of our findings in an analysis of the size dependence of the flow stress of a bioinspired nanocomposite.
A universal design paradigm in biology is the use of hierarchies, which is evident in the structu... more A universal design paradigm in biology is the use of hierarchies, which is evident in the structure of proteins, cells, tissues, and organisms, as well as outside the material realm in the design of signaling networks in complex organs such as the brain. A fascinating example of a biological structure is that of diatoms, a microscopic mineralized algae that is mainly composed of amorphous silica, which features a hierarchical structure that ranges from the nano-to the macroscale. Here, we use the porous structure found at submicron length scales in diatom algae as a basis to study a bioinspired nanoporous material implemented in crystalline silica. We consider the mechanical performance of two nanoscale levels of hierarchy, studying an array of thin-walled foil silica structures and a hierarchical arrangement of foil elements into a porous silica mesh structure. By comparing their elastic, plastic, and failure mechanisms under tensile deformation, we elucidate the impact of hierarchies and the wall width of constituting silica foils on the mechanical properties, by carrying out a series of large-scale molecular dynamics (MD) simulations with the first principles based reactive force field ReaxFF. We find that by controlling the wall width and by increasing the level of hierarchy of the nanostructure from a foil to a mesh, it is possible to significantly enhance the mechanical response of the material, creating a highly deformable, strong, and extremely tough material that can be stretched in excess of 100 pct strain, in stark contrast to the characteristic brittle performance of bulk silica. We find that concurrent mechanisms of shearing and crack arrest lead to an enhanced toughness and are enabled through the hierarchical assembly of foil elements into a mesh structure, which could not be achieved in foil structures alone. Our results demonstrate that including higher levels of hierarchy are beneficial in improving the mechanical properties and deformability of intrinsically brittle materials. The findings reported here provide insight into general material design approaches that may enable us to transform a brittle material such as silicon or silica into a ductile, yet strong and tough material, solely through alterations of its structural arrangement at the nanoscale.
We model a single crystal of silicon approaching dimensions of 20 nm × 20 nm × 10 nm with up to 2... more We model a single crystal of silicon approaching dimensions of 20 nm × 20 nm × 10 nm with up to 200,000 atoms based on the ReaxFF first principles based reactive force field, applied here to examine the influence of crack tip heterogeneities on the nucleation of dislocations from crack tips as the temperature is increased well beyond 1000 K. Our study aims at generating insight into mechanisms of the brittle-toductile transition (BDT) observed in silicon, which is known to change the behavior of silicon crystals from predominantly brittle at low temperatures to ductile at higher temperatures, likely involving a competition between brittle bond-breaking and emission of dislocations. We first examine the crystallographic orientations most widely known to exhibit fracture, for example failure on the {1 1 1} and {1 1 0} planes. We find that even at very high temperatures considered here (around 1500 K), the material behaved in a completely brittle manner for systems with cracks oriented in the {1 1 1} and {1 1 0} planes. In contrast, when the crack plane is changed to the {1 0 0} orientation, the formation of complete dislocation loops is observed. The results reported in our paper is the first direct observation of dislocation loops in silicon driven by an increase in the temperature, and extends earlier studies that were focused solely on extremely thin quasi-two-dimensional models. We demonstrate here that the formation of these loops can be linked to the geometrical ledges at the crack tip with favorable orientations for slip on the {1 1 1} planes. The detailed mechanisms leading to the nucleation of dislocations involve changes at the crack tip with bond rotations and formation of ledges, and we find that the emergence of dislocations causes the crack to arrest, but re-initiation takes place and no conclusive nucleation of dislocations and complete arrest of the crack is observed. The thickness effect is discussed together with other sources for formation of ledges along the crack front. Our findings provide important insight towards the development of models for the brittle-ductile-transition in silicon and potentially other materials, and emphasize on the significance of thickness effects in simulations of fracture in crystal slabs.
Journal of Computational and Theoretical Nanoscience, 2010
The recent discovery of single graphene sheets and the remarkable technologies envisioned for gra... more The recent discovery of single graphene sheets and the remarkable technologies envisioned for graphene-based materials necessitate the ability to assemble and reproduce nano-precise graphene structures. Here we demonstrate an approach to create atomically precise single graphene structures by applying tensile load to single sheets of graphene that feature specific patterns of vacancies. We report a computational nanoengineering approach that utilizes the first principles based reactive force field potential (ReaxFF), applied here to simulate the fracture mechanics of up to 40,000 fully reactive atoms. We find that the direction and dynamical behavior of graphene fracture can be controlled by the presence of atomistic defects in the form of atomic vacancies placed throughout the sheet. We find that these vacancies produce distinct effects on the resulting fracture surface geometries, defined by the specific patterns in which they occur throughout the 2D structure. For instance, we are able to cut graphene sheets along controlled zigzag patterns on the nanoscale using specific arrangements of vacancies. These findings suggest novel possibilities aimed at cutting and producing atomically precise graphene structures, enabling advances in graphene nanotechnology. The study reported here is the first to apply ReaxFF to model fracture of graphene sheets.
Journal of Algorithms & Computational Technology, 2008
We report a novel multi-paradigm multi-scale approach based on a combination of the first princip... more We report a novel multi-paradigm multi-scale approach based on a combination of the first principles ReaxFF force field with an empirical Tersoff potential. Our hybrid multi-scale simulation model is computationally efficient and capable of treating thousands of atoms with QM accuracy, extending our ability to simulate the dynamical behavior of a wider range of chemically complex materials such as silicon, silica and metal-organic compounds. It is implemented in the Python based Computational Materials Design Facility (CMDF). We exemplify our method in a study focused on a systematic comparison of the fracture dynamics in silicon under mode II shear versus mode I tensile loading. We find that the mode II crack tends to branch at an angle of approximately 45 degrees once the crack speed approaches 38% of the Rayleigh-wave speed. In contrast, the mode I crack continuously propagates in the direction of the initial crack, and only makes a slight change of direction towards 10 degrees once fracture instabilities occur. Our results reveal fundamental differences of fracture dynamics under mode I versus mode II loading.
International Journal for Multiscale Computational Engineering, 2007
ABSTRACT Prediction of the deformation behavior of metals in the presence of environmentally embr... more ABSTRACT Prediction of the deformation behavior of metals in the presence of environmentally embrittling species like water or hydrogen, or under presence of organic reactive chemicals, remains a critical challenge in materials modeling. Here we propose a ...
Graphene features unique electronic, thermal, and mechanical properties, and the flexibility and ... more Graphene features unique electronic, thermal, and mechanical properties, and the flexibility and strong attraction between graphene layers promotes the formation of self-folded nanostructures. Here we study the self-folding of mono-and multilayer graphene sheets, ...
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Papers by Dipanjan Sen