Query: directed evolution bring silicon to life

Candidate papers:

abstract: Bringing carbon silicon bonds to life Organic compounds containing silicon are important for a number of applications, from polymers to semiconductors. The catalysts used for creating carbon silicon bonds, however, often require expensive trace metals or have limited lifetimes. Borrowing from the ability of some metallo enzymes to catalyze other rare carbene insertion reactions, Kan et al. used heme proteins to form carbon silicon bonds across a range of conditions and substrates (see the Perspective by Klare and Oestreich) Directed evolution experiments using cytochrome c from Rhodothermus marinus improved the reaction to be 15 times more efficient than industrial catalysts. Science, this issue p. 1048; see also p. 970 Heme proteins can catalyze the formation of carbon silicon bonds. Enzymes that catalyze carbon silicon bond formation are unknown in nature, despite the natural abundance of both elements. Such enzymes would expand the catalytic repertoire of biology, enabling living systems to access chemical space previously only open to synthetic chemistry. We have discovered that heme proteins catalyze the formation of organosilicon compounds under physiological conditions via carbene insertion into silicon hydrogen bonds. The reaction proceeds both in vitro and in vivo, accommodating a broad range of substrates with high chemo and enantioselectivity. Using directed evolution, we enhanced the catalytic function of cytochrome c from Rhodothermus marinus to achieve more than 15 fold higher turnover than state of the art synthetic catalysts. This carbon silicon bond forming biocatalyst offers an environmentally friendly and highly efficient route to producing enantiopure organosilicon molecules.
author_names: S B Jennifer Kan

Russell D Lewis

Kai Chen

Frances H Arnold
title: Directed evolution of cytochrome c for carbon silicon bond formation: Bringing silicon to life
venue: Science
year: 2016

abstract: Tailor made: Discussed herein is the ability to adapt biology's mechanisms for innovation and optimization to solving problems in chemistry and engineering. The evolution of nature's enzymes can lead to the discovery of new reactivity, transformations not known in biology, and reactivity inaccessible by small molecule catalysts.
author_names: Frances H Arnold
title: Directed Evolution: Bringing New Chemistry to Life
venue: Angewandte Chemie
year: 2018

author_names: Frances H Arnold
title: Inside Cover: Directed Evolution: Bringing New Chemistry to Life (Angew. Chem. Int. Ed. 16/2018)
year: 2018

abstract: The directed evolution of enzymes is now routinely used to develop new catalysts with various applications, such as in environmentally friendly production of chemicals and renewable fuels. In her Nobel lecture, F. Arnold describes how lessons from nature inspired the development of methods for directed evolution.
author_names: Frances H Arnold
title: Innovation by Evolution: Bringing New Chemistry to Life (Nobel Lecture)
venue: Angewandte Chemie
year: 2019

abstract: Heme proteins have recently been demonstrated to catalyze cyclopropanation reactions via a putative carbene transfer mechanism. Carbene transfer reactions are not known to occur in natural biological systems, but are highly useful synthetic reactions. There is growing interest in developing new "carbene transferases" that bring new chemical reactions into the realm of biology, and growing interest in engineering these enzymes for use in organic synthesis. Additionally, the mechanistic details of iron porphyrin catalyzed carbene transfer reactions are largely unknown, especially with regards to how the enzyme environment influences the outcome of a carbene transfer reaction. This thesis details both the engineering of carbene transferases with novel catalytic capabilities and investigations into how these enzymes catalyze carbene transfer reactions. Chapter 1 introduces heme protein catalyzed carbene transfer reactions and describes the directed evolution of new enzymes that allow access to a range of useful cyclopropane products. Chapter 2 describes the evolution of an enzyme that performs carbene transfer to silicon hydrogen bonds, resulting in a highly efficient and selective carbon silicon bond forming enzyme, the first of its kind. Chapter 3 focuses on the characterization of a key reactive intermediate, the iron porphyrin carbene, in the active site of the evolved carbon silicon bond forming enzyme. This study provides an explanation of the remarkable enantioselectivity of the enzyme and provides a foundation from which to investigate the enzyme reaction mechanism. The mechanism of carbon silicon bond formation is elucidated in Chapter 4, and the is then used to explain how the enzyme achieves chemoselectivity, which in turn guides the evolution of enzyme variants with altered chemoselectivity. Finally, two off cycle catalytic pathways that cause inactivation of the carbene transferase are characterized, and methods to prevent and/or circumvent inactivation are investigated (Chapter 5) Overall, the work presented here expands the repertoire of enzyme catalyzed reactions and facilitates the continuing development of new carbene transferases by developing our mechanistic understanding of this novel class of enzymes.
author_names: Russell D Lewis
title: Evolution and Characterization of Carbene Transferases for Cyclopropanation and Carbon Silicon Bond Formation
year: 2019

abstract: The rampant use of plastics and their disposal into waste are adding to the problems of pollution. The resistance of plastics to bio degradation is an added advantage for its significant use but the same property creates havoc when the plastic products are disposed off as waste in massive amounts. The property of micro organisms to evolve quickly brings answers to even the most impossible situations. The current and several other reports show that the plastic is bio degradable. The current report shows the action of consortia of microbes isolated from a plastic dumping site can lead to degradation of the polymer. The microbial consortia isolated from plastic dumping site when made to grow in controlled conditions in presence of basal media with plastic as sole source of carbon for an extended period of time, aberrations were observed on surface of the plastic. The proteins reported till date in plastic degradation when analysed in silico for their homologs in all domains of life, they were found to be significantly similar to proteins of cutinase, hydrolase, lipase and some hypothetical proteins. This shows that the plastic degrading proteins have possibly evolved from these protein families.
author_names: Gurpreet Kaur Sidhu

Pooja Chandel
title: The microbial consortia directed evolution towards plastic degradation the key to waste management?
venue: JOURNAL OF ADVANCES IN BIOLOGY
year: 2019

abstract: An independent integrated cost and schedule life cycle risk analysis has been used to compare the viability of two competing tunneling options even at different levels of design maturity. This paper describes the process used to provide the Santa Clara Valley Transportation Authority (VTA) with a comprehensive decision making basis using comparative risk profiles for two tunneling alternatives; a single large diameter tunnel versus two smaller twin tunnels to extend San Francisco's Bay Area Rapid Transit (BART) service into downtown San Jose. VTA also conducted a fact finding mission along with BART to Barcelona's Metro Line 9 (L9) subway to allow first hand evaluation of a single bore system. Construction and system risks were qualitatively assessed and quantified in terms of cost and time to compare the cost and duration of the two options, including the differences in Operations Maintenance (O&M) costs for the first thirty years of operation. VTA selected Aldea Services, LLC (Aldea) to conduct an independent risk assessment to better inform the decision making process between the SB and TB tunneling options. The alternative configurations under consideration are a TB tunnel system and a deeper SB tunnel system. A risk assessment comparison was part of VTA's selection process to determine the preferred tunneling alternative. The assessment analyzed, described and compared the qualitative and quantitative risks associated with the two tunneling alternatives. The assessment was carried out within a risk management framework that is intended to proceed throughout design and construction in accordance with the Guidelines for Improved Risk Management on Tunnel and Underground Construction Projects in the United States of America (O'Carroll and Goodfellow, 2015) Figure 1. Phase II Extension (Source: VTA BSV Phase II Tech Studies, 2017) 2 TUNNEL ALTERNATIVES The two options are the twin bore (TB) option which constructs two single track 20 foot outer diameter subway tunnels, similar to other tunnels in the BART system, and the single bore (SB) option which constructs a single 45 foot external diameter subway tunnel that is designed to carry two tracks within the same tunnel, using a dividing wall between the trackways. Both alternatives are shown in Figure 2. 2.1 Twin bore alternative The TB design consists of two circular tunnels constructed by two TBMs to interconnect the open cut stations, mid tunnel vent structures and portals. The tunnels will be connected to each other by cross passages at regular intervals along the alignment. The project has three proposed underground stations in the 65% Preliminary Engineering Phase; Alum Rock, Downtown San Jose station and Diridon/Arena station. 2.2 Single bore alternative In addition to the feasibility study which found no fatal flaws, several follow on SB technical studies performed more detailed evaluations of the SB tunnel option and indicated that a minimum internal diameter of 41 feet was desirable to meet the minimum clearances and vehicle envelopes stipulated in the BART Facilities Standards (BFS) through all of the necessary guideway configurations and transitions along the project alignment (VTA BSV Phase II Tech Studies, 2017) During early inter agency coordination discussions, BART indicated a preference for side byside rather than stacked track configuration in the running track alignment. This arrangement required transitions from side by side running tunnel to the over/under configuration at the stations which controlled the diameter because the maximum open space was needed to facilitate the transitions. The SB Feasibility Study concluded a minimum depth of cover of 65 feet for the SB tunnel. Subsequent technical studies with more detailed evaluations indicated that a shallower minimum cover depth of 50 feet was constructible and appropriate for further evaluation of a SB tunnel as the design progressed (VTA BSV Phase II Tech Studies, 2017) Figure 2. Twin Bore (TB) and Single Bore (SB) tunnel alternatives (Source: VTA Board Workshop and General Public Final Review, Sept 22, 2017) 2.3 VTA and BART representatives travel to Spain to inspect Barcelona's Metro Line 9 single bore system One of VTA's commitments to BART was to fully investigate the life cycle impacts in any evaluation made of the Twin Bore and Single Bore options; not simply to assess the initial constructability impacts. At the forefront of these considerations for BART, as it would be for any subway system operator, was long term Operation and Maintenance. Getting a first hand account of how a Single Bore system actually works in practice and how difficult it was to service and maintain was no easy task since there were no SB systems in North America. To do this properly would mean travelling to the first such system built in the world; Barcelona's Line 9 (L9) in Spain. In addition to be the longest working SB system, Barcelona met the other essential criteria; they also operated a major network of older non SB lines (like BART) so they had the ability to make valid comparisons between operating both types of systems. The ability to allow both BART and VTA staff to inspect the L9 first hand, meet their counterparts in Barcelona, ask questions and engage in free ranging discussion, led VTA officials to make the effort to bring all these people and experiences together. This culminated in a trip to Barcelona by VTA and BART staff for this purpose in July of 2017. BART's Observations: BART's review paid particular attention to Line 9's technology requirements, how the system was staffed, and security aspects of line. BART observed that L9 required less service labor due to more automation (for example, trains are driverless) BART learned that L9 has roving staff covering multiple stations for station operations and maintenance. VTA's Observations: VTA meet with L9 officials and found out that the same challenges of working in a dense urban environment with deep stations (very deep in Barcelona's case) that were not amenable to cut cover excavation, were the same issues that first led Barcelona to investigating SB for L9. These same officials confirmed that when these conditions combined, significant cost efficiencies were able to be achieved by utilizing an SB configuration. VTA was impressed with some new features they had not encountered before, particularly the use of Platform Automatic Screen Doors as well as the use of numerous High Speed Elevators (great for deep stations) VTA made notes of these features (including their own idea of optimizing the timing of elevators for the arrival/departure of trains) and is currently exploring the benefits of incorporating these improvements into the BSV Phase II design. VTA learned that Barcelona created an 'open' system for L9 O&M Training. They provided everyone a chance to learn O&M for the SB L9 system, but it was completely voluntary. Reviews of this practice were favorable throughout Barcelona's organization. VTA observed a lot of young people, both staff and engineers, that when interviewed said they loved the challenges of working on something new. VTA investigated the performance of L9's Emergency Exits. During one of their site visits to a deep station, they went through one of the Emergency Exits and travelled to the surface. VTA noted that L9 has emergency ramps (not staircases) and that these deposited into a defined rescue area on the surface (as opposed to the street) These features are also under study for inclusion in the final design of the stations. VTA concluded that the L9 system functions efficiently, even with deeper stations than those planned for San Jose. The trip was an important milestone in the selection process. It allowed critics to ask "unfiltered" questions directly to the people involved with running a SB system and receive direct answers to those questions. It allowed both BART and VTA to both tangibly vet as well as look "under the hood" of a system that did not exist in North America as well as get a first hand account of the realities of maintaining such a system. While it would be incorrect to say that views were changed by the trip, it was critical in removing the abstractive veil surrounding the SB option and sharpened the focus of all parties on the task of evaluating the physical/operational issues that differed between the options. 2.4 Risk assessment process An integrated cost and schedule analysis seeks to identify all risks and uncertainties that might significantly affect the predicted project cost and schedule. Specific methods are used to quantify what each of those impacts might be by using estimates of minimum, most likely and maximum values of cost and schedule. A numerical simulation model aggregates these impacts to risk based cost and risk loaded schedule results that are probabilistic distributions (instead of deterministic single value only estimates) 2.5 Qualitative analysis The comparative risk assessment process for cost and schedule first reviewed and evaluated comparative base costs for both alternatives and normalized the costs of both options to a common date (December 31, 2016 in this case) Next, a workshop process was used, including stakeholders (such as BART, VTA, the City of San Jose etc. and nationally recognized subject matter experts to identify risks and uncertainties that might significantly affect the predicted project cost and schedule for both options. Risk assessment workshops were used to: Identify significant potential events and conditions (both risks/threats and opportunities) that could affect project cost and schedule. Assess risk impacts and likelihoods. Develop an integrated initial cost and schedule risk register and then identify and discuss mitigation measures for significant risk components and estimate the potential risk reduction from each mitigation measure together with the residual risk after mitigation as shown in Figure 5. Identify, d
author_names: K Davey

A Moergeli

J J Brady

Saqib Ahmad Saki

Ryan Goodfellow

Ana del Amo
title: Bart Silicon Valley Phase II integrated cost schedule life cycle comparative risk analysis of single bore versus twin bore tunneling
venue: Tunnels and Underground Cities: Engineering and Innovation meet Archaeology, Architecture and Art
year: 2019

abstract: Significance Organisms are known to invest resources to disperse their offspring. Plants produce fruits, although fruit eaters do not promise to disperse seeds to the right places. According to a classical theory, costly dispersal can evolve because dispersing individuals can avoid competition among their own offspring. The textbook formulas of evolutionary stable dispersal strategies, however, assume the same living conditions everywhere. Here we present formulas predicting the dispersal probability in spatially heterogeneous environments. In the real world, no environment is homogeneous as assumed in the classical theory, so our results bring in important achievements. In heterogeneous environments the evolved dispersal probability can be much lower than in homogeneous ones, and also diversification in dispersal strategies is possible. Dispersal is one of the fundamental life history strategies of organisms, so understanding the selective forces shaping the dispersal traits is important. In the Wright's island model, dispersal evolves due to kin competition even when dispersal is costly, and it has traditionally been assumed that the living conditions are the same everywhere. To study the effect of spatial heterogeneity, we extend the model so that patches may receive different amounts of immigrants, foster different numbers of individuals, and give different reproduction efficiency to individuals therein. We obtain an analytical expression for the fitness gradient, which shows that directional selection consists of three components: As in the homogeneous case, the direct cost of dispersal selects against dispersal and kin competition promotes dispersal. The additional component, spatial heterogeneity, more precisely the variance of so called relative reproductive potential, tends to select against dispersal. We also obtain an expression for the second derivative of fitness, which can be used to determine whether there is disruptive selection: Unlike the homogeneous case, we found that divergence of traits through evolutionary branching is possible in the heterogeneous case. Our numerical explorations suggest that evolutionary branching is promoted more by differences in patch size than by reproduction efficiency. Our results show the importance of the existing spatial heterogeneity in the real world as a key determinant in dispersal evolution.
author_names: Kalle Parvinen

Hisashi Ohtsuki

Joe Yuichiro Wakano
title: Evolution of dispersal in a spatially heterogeneous population with finite patch sizes
venue: Proceedings of the National Academy of Sciences
year: 2020

abstract: Abstract Integrated silicon nanophotonics has rapidly established itself as intriguing research field, whose outlets impact numerous facets of daily life. Indeed, nanophotonics has propelled many advances in optoelectronics, information and communication technologies, sensing and energy, to name a few. Silicon nanophotonics aims to deliver compact and high performance components based on semiconductor chips leveraging mature fabrication routines already developed within the modern microelectronics. However, the silicon indirect bandgap, the centrosymmetric nature of its lattice and its wide transparency window across optical telecommunication wavebands hamper the realization of essential functionalities, including efficient light generation/amplification, fast electro optical modulation, and reliable photodetection. Germanium, a well established complement material in silicon chip industry, has a quasi direct energy band structure in this wavelength domain. Germanium and its alloys are thus the most suitable candidates for active functions, i.e. bringing them to close to the silicon family of nanophotonic devices. Along with recent advances in silicon germanium based lasers and modulators, short wave infrared receivers are also key photonic chip elements to tackle cost, speed and energy consumption challenges of exponentially growing data traffics within next generation systems and networks. Herein, we provide a detailed overview on the latest development in nanophotonic receivers based on silicon and germanium, including material processing, integration and diversity of device designs and arrangements. Our Review also emphasizes surging applications in optoelectronics and communications and concludes with challenges and perspectives potentially encountered in the foreseeable future.
author_names: Daniel Benedikovic

Leopold Virot

Guy Aubin

Jean-Michel Hartmann

Farah Amar

Xavier Le roux

Carlos Alonso-Ramos

Eric Cassan

Delphine Marris-Morini

Jean-Marc Fedeli

Frederic Boeuf

Bertrand Szelag

Laurent Vivien
title: Silicon germanium receivers for short wave infrared optoelectronics and communications
year: 2020

abstract: Integrated silicon nanophotonics has rapidly established itself as intriguing research field, whose outlets impact numerous facets of daily life. Indeed, nanophotonics has propelled many advances in optoelectronics, information and communication technologies, sensing and energy, to name a few. Silicon nanophotonics aims to deliver compact and high performance components based on semiconductor chips leveraging mature fabrication routines already developed within the modern microelectronics. However, the silicon indirect bandgap, the centrosymmetric nature of its lattice and its wide transparency window across optical telecommunication wavebands hamper the realization of essential functionalities, including efficient light generation/amplification, fast electro optical modulation, and reliable photodetection. Germanium, a well established complement material in silicon chip industry, has a quasi direct energy band structure in this wavelength domain. Germanium and its alloys are thus the most suitable candidates for active functions, i.e. bringing them to close to the silicon family of nanophotonic devices. Along with recent advances in silicon germanium based lasers and modulators, shortwave infrared receivers are also key photonic chip elements to tackle cost, speed and energy consumption challenges of exponentially growing data traffics within next generation systems and networks. Herein, we provide a detailed overview on the latest development in nanophotonic receivers based on silicon and germanium, including material processing, integration and diversity of device designs and arrangements. Our Review also emphasizes surging applications in optoelectronics and communications and concludes with challenges and perspectives potentially encountered in the foreseeable future.
author_names: Daniel Benedikovic

Leopold Virot

Guy Aubin

Jean-Michel Hartmann

Farah Amar

Xavier Le Roux

Carlos Alonso-Ramos

Eric Cassan

Delphine Marris-Morini

Jean-Marc Fedeli

Frederic Boeuf

Bertrand Szelag

Laurent Vivien
title: Silicon germanium receivers for short waveinfrared optoelectronics and communications High speed silicon germanium receivers (invited review)
year: 2020