Mapping behavioral specifications to model parameters in synthetic biology

With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal design specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified design constraints are robustly satisfied. In this work we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction. The method is general and can hence be incorporated in a pipeline for the rational forward design of arbitrary devices in synthetic biology

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods