John McCaskill
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John S McCaskill (born 1957 in Sydney, Australia, D.Phil. Oxford, 1982 in Theoretical Chemistry) works in a wide variety of fields ranging from theoretical biochemistry to novel computation to artificial life.
Biography
After graduating from Sydney University in 1978 (R.G. Gilbert advisor) and obtaining his PhD (D. Phil.) in 1982 as a Rhodes Scholar at New College, Oxford, McCaskill joined the group of Nobel prize-winner Manfred Eigen at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany, where he was awarded a Max Planck travel scholarship, taken up at UC San Diego, and then a QEII Fellowship to return to Australia, visiting Sidney University 1985-1987.
He returned to the Max Planck Institute for Biophysical Chemistry as a group leader in 1987, and subsequently held positions at the Institute for Molecular Biotechnology Jena and Professor for Theoretical Biochemistry at the Friedrich Schiller University Jena, at the GMD (National Research Center for Information Technology, , the Fraunhofer Society, Ruhr University Bochum, the Santa Fe Institute, and the European Center for Living Technology at the Ca' Foscari University of Venice.
Research
McCaskill is best known for his work on information processing in evolving and self-organizing molecular systems, spanning theoretical and experimental approaches including novel devices and systems. In the last 15 years, he has established a chemical microprocessor technology for electronically programmable matter via microscale electrochemistry, and applied it to the development of novel approaches towards artificial cells and DNA processing systems. [1] Most recently his research has led to the development of novel autonomous and programmable electronic-chemical [2] microparticles (lablets [3] ) opening a wide range of potential applications in basic and applied research.
Over the past 35 years McCaskill has contributed to the theory of molecular evolution and introduced the experimental study of microscale spatially-resolved chemical evolution. He developed an ensemble approach to RNA structure prediction, now in wide use, and the first reconfigurable computing hardware to simulate long-term chemical evolution. He developed microfluidic systems for analysing biomolecular evolution and developed the first programmable in vitro ecosystems based on DNA – some of the earliest examples of synthetic biology. He designed and implemented an optically programmable DNA computer using microfluidics and an electronically programmable biomolecular processor using microsystem technology. This seeded an international initiative to investigate electronically evolvable artificial chemical cells. As part of these efforts McCaskill led EU projects PACE and MICREAgents. McCaskill's current work includes modeling the essential interplay of self-organization and evolution in life-like chemical systems, and exploring the potential of electronic-chemical hybrid Information Technology based on these properties. He has produced over 100 scientific publications, taught courses and supervised PhD theses in disciplines ranging from chemistry, physics and biology to computer science, and his multidisciplinary work straddling theory and experiment has been recognized in invited lectures at international conferences around the world. He was an inaugural director of the European Center for Living Technology, and has since served on its science board. While McCaskill’s main work is in basic science, it has helped spawn several start-up companies and continues to involve the coordination of major collaborative projects fostering novel links between science and industry.
Research areas
Irreversible dynamics of atoms and molecules
First example of inertial friction for intramolecular dynamics in solution identified (for the molecule 1,1’-binapthyl) extending Kramers’ theory to angular motion, with Robert Gilbert (Hons Thesis supervisor). [4] First consistent theoretical treatment accounting for quantum bound states in electronic transport theory, delivering expressions for atomic friction and electronic resistivity, and thereby contributing to our understanding of the origin of irreversible dynamics in quantum mechanics, with Norman March (PhD supervisor). [5] Novel multipolar dissipative particle dynamics algorithm, designed with Rudolf Füchslin and Thomas Maeke, to simulate amphiphilic systems forming structures like membranes and micelles and applied to studying endocytosis in liver cells (German Hepatosys Project) and to evolving amphiphilic systems. [6]
Equilibrium statistical mechanics of DNA and RNA
Analytical solution for the asymptotic distribution of ions around polyelectrolytes like DNA in aqueous salt solution, found by applying inverse monodromy theory to the ODE Painlevé III, with Edward Fackerel. [7] Prediction of RNA secondary structure ensembles via the partition function and hence the equilibrium probability of base pairings (using an O(N^3) dynamic programming algorithm). In contrast with the Zuker algorithm, predicting only the minimal free energy structure, the new algorithm showed for the first time that many biological RNA sequences fold into an ensemble of multiple structures. [8] [9]
Molecular Evolution Theory: Quasispecies & Beyond
Molecular Quasispecies formulation and formalization, with Manfred Eigen and Peter Schuster. [10] [11] Renormalization of Manfred Eigen’s quasispecies theory for the evolution of molecular information: predicting localized quasispecies even with continuous fitness distributions. [12] Development of stochastic quasispecies theory, showing the slowing down of evolutionary optimization with time and the population size dependence of the error threshold. [13] Application of extreme value theory to predict the course of evolutionary optimization in quasispecies theory, with Manfred Eigen and Peter Schuster. [11] Algorithmic formulation of the evolution of interacting molecules as a generalization of Turing machines with head-tape recognition. “Polymer Chemistry on Tape.” [14] First molecular graph grammars for studying combinatorial DNA amplification systems and their evolution with Ulrich Niemann. [15] Design and construction of first reconfigurable computer (NGEN) using a large array of FPGAs to study spatial molecular evolution using compact moving data bitstream processors in digital logic, and as an early example of evolvable hardware, with Thomas Maeke and Udo Gemm. [16] First demonstration of the possibility of evolving genetic coding in 3D spatially resolved systems, with Rudolf Füchslin and Thomas Maeke. [17], making use of the custom built, third generation, massively parallel, reconfigurable computer MEREGEN, designed and built together with Uwe Tangen and Thomas Maeke. [18] Analytical results on stochastic evolution of spatial cooperative systems using a projection from infinite dimensional space, including the demonstration that folding stabilizes the cooperative evolution of catalysts, with Stefan Altmeyer and Rudolf Füchslin. [19] Genetic self-assembly, a demonstration of the power of coupling self-assembly and evolution via genetically encoding a limited number of functional entities together with their recognition properties, applied with Rudolf Füchslin and Thomas Maeke to the problem of evolving multiplication circuits from examples using inductive generalization and coevolution with tasks. [20] First simulation (evoself) of the spatial evolution of (genetic) combinatorial amphiphiles, using spin-lattice models (generalizing the Widom model) with Norman Packard, Steen Rasmussen and Mark Bedau. [21]
Spatial Evolution: Experiments
Prediction, theory, and (with Günter Bauer and Hajo Otten) discovery of RNA travelling waves as ideal evolution reactors 1989 and their application of these to collect statistics on RNA evolution with Günter Bauer, to viral systems with John Yin, and other amplification systems with J. Dapprich. [22] Design of first microfluidics systems as open spatially resolved flow reactors for studying evolution, with Kristina Schmidt and Petra Foerster. [23] Earliest synthetic biology approach to studying evolution in interacting molecular systems including the design and construction of a molecular predator-prey (with Britta Wlotzka) and cooperative system CATCH (with Ralf Ehricht and Thomas Ellinger) using DNA, RNA and various enzymes. [24] Simulation of spatial pattern formation in these first spatial synthetic biology experimental systems capable of evolution with Jens Breyer, Jörg Ackermann, Thomas Kirner, Bert Böddeker, R. Ehricht. [25]
Microfluidic control of Molecular Information Processing
Design and construction of first single molecule tracking system based on novel fluorescence imaging (with Malte Köllner, Birgit Wagner, Harald Mathis, and Uwe Tangen) involving a specially designed MCP (multi-channel-plate detector) developed by Proxitronic GmbH and a custom designed xy-particle detector developed by Peter Fischer and colleagues in Norbert Wermes group at Univ. Bonn. 1995-2001. Design and construction (with Danny van Noort, Patrick Wagler, and others) of first optically programmable DNA computer prototype using microfluidics and magnetic beads. [26] Design and construction of a programmable nanoliter scale droplet generator for combinatorial DNA library exploration, with Uwe Tangen, Patrick Wagler and Abhishek Sharma. [27]
Electronic Microsystems towards Artificial Cells & Smart Lablets
First demonstration of programmable electronic microfluidic concentrator exploiting opposing electrophoresis and electroosmosis effects for charged molecules such as DNA, with Uwe Tangen, Patrick Wagler and Goran Goranovic. [28] Programmable artificial cell evolution (PACE) system prototype involving microfluidic life support, employed in studies towards the integration of the three chemistries required for artificial cells (genetic, metabolic and container chemistry), idea developed with Norman Packard, Steen Rasmussen and Mark Bedau, implementation developed with Patrick Wagler and Uwe Tangen. [29] Design of electronic microfluidic systems to implement an electronic chemical cell, combining molecular amplification and separation processes together with Uwe Tangen, Patrick Wagler. [30] Conception and implementation of a continuous droplet flow architecture with upstream backcoupling of DNA as renewable matrix for chemical information technology (MATCHIT) with Patrick Wagler, Uwe Tangen, Thomas Maeke, Antonio Minero and Steen Rasmussen. 2012 EU Project MATCHIT 2010-2013. Lead design and implementation of autonomous microscale electronic chemical reagent particles (lablets [3]) based on a programmable CMOS substrate (MICREAgents, 2012) together with 10 project partners. Design and construction of differential galvanic coating apparatus for combinatorial CMOS and electrode coating on silicon wafers, together with Abhishek Sharma, Thomas Maeke and Lukas Straczek. [31]
References
- ↑ Cf. DNA replication, DNA repair, DNA polymerase, RNA editing, Restriction enzymes.
- ↑ Electronic-chemical: A novel combination of electronics and chemistry, combining electronic chips with electrochemical, electrokinetic (e.g. electroosmotic) or electrostatic (e.g. electrowetting) actuators and sensors.
- ↑ 3.0 3.1 Lablets: programmable microscale chemically reactive electronic particles that can serve as autonomous miniature labs performing chemical analysis, regulation or synthetic tasks.
- ↑ Füchslin, R. M., Maeke, T., & McCaskill, J. S. (2009). Spatially resolved simulations of membrane reactions and dynamics: Multipolar reaction DPD. The European Physical Journal E, 29(4), 431–448. doi: 10.1016/0301-0104(79)85222-2
- ↑ 1984 doi: 10.1016/0022-3697(84)90121-5
- ↑ 2009 doi: 10.1140/epje/i2009-10482-x
- ↑ "Painlevé solution of the poisson-boltzmann equation for a cylindrical polyelectrolyte in excess salt solution", John S. McCaskill and Edward D. Fackerell ,J. Chem. Soc., Faraday Trans. 2, 1988,84, 161-179 doi: 10.1039/f29888400161
- ↑ 1990 doi: 10.1002/bip.360290621,pp 13-24 in ISSN 0175-7571,
- ↑ doi: 10.1007/978-3-642-77798-1_3
- ↑ Eigen, Manfred, John McCaskill, and Peter Schuster. "Molecular quasi-species." The Journal of Physical Chemistry 92.24 (1988): 6881-6891.
- ↑ 11.0 11.1 Eigen, Manfred, John McCaskill, and Peter Schuster. "The molecular quasi-species." Adv. Chem. Phys 75 (1989): 149-263. 1988 doi: 10.1002/9780470141243.ch4
- ↑ McCaskill, JS "A Localization Threshold for Macromolecular Quasispecies from Continuously Distributed Replication Rates" Journal of Chemical Physics (1984) 80(10) 5194-5202. doi
- ↑ McCaskill, JS "A Stochastic-Theory of Macromolecular Evolution" Biological Cybernetics (1984) 50(1) 63-73. doi
- ↑ J. McCaskill (1988). "Polymer Chemistry on tape: A computational model for emergent genetics." Internal report, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany.
- ↑ Steady Flow Micro-Reactor Module for Pipelined DNA Computations John S. McCaskill, Robert Penchovsky, Marlies Gohlke, Jörg Ackermann, and Thomas Rücker p. 263-270. in Condon, A., and G. Rozenberg. "DNA Computing." (2001). doi: 10.1007/3-540-44992-2.
- ↑ 1992-1994 Patent DE19934335690 , Doi: 10.1002/bbpc.19940980906
- ↑ 2001 Doi: 10.1073/pnas.151253198
- ↑ Tangen, U., Th Maeke, and J. S. McCaskill. "Advanced simulation in the configurable massively parallel hardware MereGen." Coupling of Biological and Electronic Systems. Springer, Berlin, Heidelberg, 2002. 107-118.
- ↑ 2001-2004 Doi: 10.1073/pnas.151253198,Doi: 10.1515/bc.2001.167,Doi: 10.1162/106454604322875896
- ↑ Füchslin, Rudolf M., et al. "Evolving inductive generalization via genetic self-assembly." Advances in Complex Systems 9.01n02 (2006): 1-29. 10.1142/s0219525906000598
- ↑ McCaskill, John S., et al. "Evolutionary self-organization in complex fluids." Philosophical Transactions of the Royal Society of London B: Biological Sciences 362.1486 (2007): 1763-1779. doi: 10.1098/rstb.2007.2069
- ↑ 1989-1994: Doi: 10.1073/pnas.86.20.7937 Doi: 10.1016/s0006-3495(92)81958-6 Doi: 10.1073/pnas.90.9.4191 Doi: 10.1002/bbpc.19940980927
- ↑ 1994, 1997 Doi: 10.1002/bbpc.19940980928 Doi: 10.1016/s0301-4622(97)00073-2.
- ↑ 1995, 1997 Doi: doi: [https://dx.doi.org/10.1016/s1074-5521(97)90234-9, doi: 10.1016/s1074-5521(97)90234-9 Doi: 10.1111/j.1432-1033.1997.0358a.x Doi: 10.1016/s1074-5521(98)90665-2
- ↑ 1994-1999 Doi: 10.1016/s0301-4622(97)00073-2, Doi: 10.1162/106454698568422,Doi: 10.1016/s0301-4622(99)00049-6
- ↑ 2001-2 Doi: 10.1016/s0303-2647(01)00099-5
- ↑ 2015 Doi: 10.1063/1.4907895 Doi: 10.1063/1.4926616
- ↑ 2006 Doi: 10.1159/000094187
- ↑ 2008 Doi: 10.1016/j.cej.2007.07.061
- ↑ 2011 Doi: 10.1016/j.biosystems.2012.01.005
- ↑ 2016. Publication pending.
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