Prof Gonen Ashkenasy Research Group - Scientific Publications

Research and Review Papers

>> H. Sadihov-Hanoch, A. K. Bandela, A. Chotera-Ouda, O. Ben David, R. Cohen-Luria, D. G. Lynn, G. Ashkenasy "Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras".Soft Matter 2023, 19, 3940-3945.

>> A. K. Bandela, H. Sadihov‐Hanoch, R. Cohen‐Luria, C. Gordon, A. Blake, G. Poppitz, D. G. Lynn, G. Ashkenasy "The Systems Chemistry of Nucleic‐acid‐Peptide Networks". Isr. J. Chem. 2022, 10, e202200030.

>> C. Glionna, V. Kumar, G. Le Saux, B. Pramanik, N. Wagner, R. Cohen-Luria, G. Ashkenasy, N. Ashkenasy “Dynamic Surface Layer Coiled Coil Proteins Processing Analog-to-Digital Information". J. Am. Chem. Soc. 2021, 143, 17441−17451.

>> I. Maity, D. Dev, K. Basu, N. Wagner, G. Ashkenasy "Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network". Angew. Chem. Int. Ed. 2021, 60, 4512-4517.

* This paper was reviewed in Chemistry Views on Nov. 24, 2020 https://www.chemistryviews.org/details/ezine/11274755/Programming_Nanoparticle_Formation_and_Assembly.html

>> A.K. Bandela, N. Wagner, H. Sadihov, S. Morales-Reina, A. Chotera-Ouda, K. Basu, R. Cohen-Luria, A. de la Escosura, G. Ashkenasy "Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks" Proceedings of the National Academy of Sciences of the United States of America, 2021, 118, 9 e2015285118

>> N. Wagner, R. Mukherjee, I. Maity, S. Kraun, G. Ashkenasy “Programming Multistationarity in Chemical Replication Networks” ChemSystemsChem. 2020, 2(2), e1900048.

- >> M. Frenkel-Pinter, M. Samanta, G. Ashkenasy, L.J. Leman“Prebiotic Peptides: Molecular Hubs in the Origin of Life” Chem. Rev. 2020, 11, 4707-4765.
>> N. Wagner, D. Hochberg, E. Peacock-Lopez & I. Maity, G. Ashkenasy "Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior." Life, 2019, 9(2), 45.
>> D. Kroiss, G. Ashkenasy, A. B. Braunschweig, T. Tuttle & R. V. Ulijn "Catalyst: Can Systems Chemistry Unravel the Mysteries of the Chemical Origins of Life?" Chem. 2019, 5, 1917-1920.
>> N. Wagner & G. Ashkenasy "Rhythm before life." Nat. Chem. 2019, 11, 681-683.
>> I. Maity, N. Wagner, R. Mukherjee, D. Dev, E. Peacock-Lopez, R. Cohen-Luria & G. Ashkenasy "A chemically fueled non-enzymatic bistable network." Nat. Commun. 2019, 10, 4636.
>> A. Chotera, H. Sadihov, R. Cohen‐Luria, P.A. Monnard, G. Ashkenasy “Functional Assemblies Emerging in Complex Mixtures of Peptides and Nucleic Acid–Peptide Chimeras" Chem. Eur. J. 2018, 24, 10128-10135.
>> Y. Bai, A. Chotera,O. Taran, C. Liang, G. Ashkenasy, D. G. Lynn “Achieving biopolymer synergy in systems chemistry" Chem. Soc. Rev. 2018, 47, 5444-5456.

>> W. Hordijk, S. Shichor, G. Ashkenasy “The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics" ChemPhysChem. 2018, 19, 2437-2444.
>> J. Nanda, B. Rubinov, D. Ivnitski, R. Mukherjee, E. Shtelman, Y. Motro,Y. Miller, N. Wagner, R.C. Luria, G. Ashkenasy “Emergence of native peptide sequences in prebioticreplication networks" Nature Commun. 2017, 8, 434.
>> G. Ashkenasy, T. M. Hermans, S. Otto, A. F. Taylor "Systems Chemistry" Chem. Soc. Rev. 2017, 46, 2543-2554. .
>> N. Wagner, R. Mukherjee, I. Maity, E. Peacock-Lopez, G. Ashkenasy "Bistability and Bifurcation in Minimal Self-replication and Non-enzymatic Catalytic Networks" ChemPhysChem. 2017, 18, 1842–1850.
>> D. Ivnitski, M. Amit, O. Silberbush, Y. Atsmon-Raz, J. Nanda, R. Cohen-Luria, Y. Miller, G. Ashkenasy, N. Ashkenasy "The Strong Influence of Structure Polymorphism on the Conductivity of Peptide Fibrils " Angew. Chem. Int. Ed. 2016, 55, 9988-9992.
* This paper was recommended by Dr. D. Lynn for the F1000 site on Aug 16, 2016. https://facultyopinions.com/prime/726489690#eval793540195
>> M. Tena-Solsona, J. Nanda, S. Díaz-Oltra, A. Chotera, G. Ashkenasy, B. Escuder "Emergent Catalytic Behavior of Self-Assembled Low Molecular Weight Peptide-Based Aggregates and Hydrogels" Chem. Eur. J. 2016, 22, 6687-6694.
>> J. Lerner Yardeni, M. Amit, G. Ashkenasy, N. Ashkenasy "Sequence Dependent Proton Conduction in Self-assembled Peptide Nanostructures" Nanoscale, 2016, 8, 2358-2366.
>> R. Mukherjee, R. Cohen-Luria, N. Wagner, G. Ashkenasy "A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template Directed Ligation" Angew. Chem. Int. Ed. 2015, 54, 12452-12456.
>> L. Gurevich, R. Cohen-Luria, N. Wagner, G. Ashkenasy "Robustness of Synthetic Circadian Clocks to Multiple Enviromental Changes" Chem. Comm. 2015, 51, 5672-5675.
>> N. Wagner, S. Alasibi, E. Peacock-Lopez, G. Ashkenasy "Coupled Oscillations and Circadian Rhythms in Molecular Replications Networks" J. Phys. Chem. Lett. 2015, 6, 60-65.
>> Z. Dadon, N. Wagner, S. Alasibi, M. Samiappan, R. Mukherjee, G. Ashkenasy "Competition and Cooperation in Dynamic Replication Networks" Chem. Eur. J. 2015, 21, 648-654.
>> G. Ashkenasy, A. Pross "Origin of Life: Special Issue Honoring Prof. Albert Eschenmoser on the Occasion of his 90th Birthday" (Editorial Assay) Isr. J. Chem. 2015, 55, 835-836.
>> N. Wagner, G. Ashkenasy "How Catalytic Order Drives the Complexification of Molecular Replication Networks" Isr. J. Chem. 2015, 55, 880-890.
>> D. Ivnitski, M. Amit, B. Rubinov, R. Cohen-Luria, N. Ashkenasy, G. Ashkenasy "Introducing Charge Transfer Functionality into Prebiotically relevant β-Sheet Peptide Fibrils" Chem. Commun. 2014, 50, 6733-6736.
>> Y. Shamay, L. Shpirt, G. Ashkenasy, A. David "Complexation of Cell-Penetrating Peptide-Polymer Conjugates with Polyanions Controls Cells Uptake of HPMA Copolymers and Anti-tumor Activity" Pharm. Res. 2014, 31, 768-779.
>> Z. Dadon, M. Samiappan, A. Shahar, R. Zarivach, G. Ashkenasy "A High-Resolution Structure that Provides Insight into Coiled-Coil Thiodepsipeptide Dynamic Chemistry" Angew. Chem. Int. Ed. 2013, 52, 9944-9947.
>> M. Eisenberg, I. Shumacher, R. Cohen-Luria, G. Ashkenasy "Dynamic Combinatorial Libraries of Artificial Repeat Proteins" Bioorg. Med. Chem. 2013, 21, 3450-3457.
>> Y. Raz, B. Rubinov, M. Matmor, H. Rapaport, G. Ashkenasy, Y. Miller "Eﬀects of Mutations in De Novo Designed Synthetic Amphiphilic β-Sheet Peptides on Self-Assembly of Fibrils" Chem. Commun. 2013, 49, 6561-6563.
>> A. Atanassov, Z. Hendler, I. Berkovich, G. Ashkenasy, N. Ashkenasy "Force Modulated Conductance of Artificial Coiled-Coil Protein Monolayers" Biopolymers: Peptide Science, 2013, 100, 1, 93–99.
>> B. Rubinov, N. Wagner, M. Matmor, O. Regev, N. Ashkenasy, G. Ashkenasy "Transient Fibril Structures Facilitating Non-Enzymatic Self-Replication" ACS nano, 2012, 6, 7893-7901.
* Selected for "Research highlights" in Nature Nanotechnology September 2012.
>> M. Samiappan, S. Alasibi, R. Cohen-Luria, A. Shanzer, G. Ashkenasy "Allosteric Effects in Coiled-Coil Proteins Folding and Lanthanide-Ion Binding" Chem. Commun. 2012, 48, 9577-9579.
* Featured in Chem. Commun. Vol. 48, issue 77 inside cover page.
>> Z. Dadon, M. Samiappan, N. Wagner, G. Ashkenasy "Chemical and Light Triggering of Peptide Networks under Partial Thermodynamic Control" Chem. Commun. 2012, 48, 1419-1421.
* Selected for publication in the ‘Emergent Investigators’ issue of Chemical Communication for January 2012.
>> M. Samiappan, Z. Dadon, G. Ashkenasy "Replication NAND Gate with Light as Input and Output" Chem. Commun. 2011, 47, 710-712.
* Selected by Chemical Communications editors as a "Hot Paper" for November 2010.
>> N. Wagner, B. Rubinov, G. Ashkenasy "β-Sheet-Induced Chirogenesis in Polymerization of Oligopeptides" ChemPhysChem. 2011, 12, 2771-2780.
>> H. Baabur, S. Dayalan, I. Shumacher, R. Cohen-Luria, G. Ashkenasy "Artificial Leucine Rich Repeats as New Scaffold for Protein Design" Bioorg. Med. Chem. Lett. 2011, 21, 2372-2375.
>> V. Bourbo, M. Matmor, E. Shtelman, B. Rubinov, N. Ashkenasy, G. Ashkenasy "Self-assembly and Self-replication of Short Amphiphilic β-sheet Peptides" Origins. Life. Evol. Bios. 2011, 41, 563-567.
>> Y. Shamay, L. Adar, G. Ashkenasy, A. David "Light Induced Drug Delivery to Cancer Cells" Biomaterials, 2011, 32, 1377-1386.
>> G. Ashkenasy, Z. Dadon, S. Alesebi, N. Wagner, N. Ashkenasy "Building Logic into Peptide Networks: Bottom-Up and Top-Down" Isr. J. Chem. (review), 2011, 51, 106 – 117.
>> N. Wagner, S. Alesebi, G. Ashkenasy "How Symmetry and Order Affect Logic Operations and Computation in Catalytic Chemical Networks" J. Comput. Theor. Nanosci. 2011, 8, 471-480.
>> Z. Dadon, M. Samiappan, E. Yishay, G. Ashkenasy, "Light-Induced Peptide Replication Controls Logic Operations in Small Networks" Chem. Eur. J. 2010, 16, 12096 – 12099.
>> N. Wagner, E. Tannenbaum, G. Ashkenasy, "Second-Order Catalytic Quasispecies Model Yields Discontinuous Mean Fitness at the Error Threshold", Phys. Rev. Lett. 2010, 104, 188101/1-188101/4.
>> C. Shlizerman, A. Atanassov, I. Berkovich, G. Ashkenasy, N. Ashkenasy, "De Novo Designed Coiled Coil Proteins with Variable Conformations as Components of Molecular Electronic Devices", J. Am. Chem. Soc. 2010, 132, 5070-5076.
>> Y. Shamay, D. Paulin, G. Ashkenasy, A. David, "Multivalent Display of Quinic Acid Ligands for Targeting E-selectin Expressing Cells", J. Med. Chem. 2009, 52, 5906-5915.
>> Y. Shamay, D. Paulin, G. Ashkenasy, A. David, "E-selectin binding peptide-Polymer-Drug Conjugates and their Selective Cytotoxicity against Vascular Endothelial Cells", Biomaterials, 2009, 30, 6460-6468.
>> B. Rubinov, N. Wagner, H. Rapaport, G. Ashkenasy, "Self Replicating Amphiphilic β-Sheet Peptides", Angew. Chem. 2009, 121, 6811-6814.
>> N. Wagner, G. Ashkenasy, "Systems Chemistry: Logic Gates, Arithmetic Units, and Network Motifs in Small Networks", Chem. Eur. J. 2009, 15, 1765-1775.
>> N. Wagner, G. Ashkenasy, "Symmetry and Order in Systems Chemistry", J. Chem. Phys. 2009, 130, 164907/1-6.
>> Z. Dadon, N. Wagner, G. Ashkenasy "The Road to Non-Enzymatic Molecular Networks", Angew. Chem. Int. Ed. 2008, 47, 6128.
>> N. Gandhi, G. Ashkenasy, E. Tannenbaum "Associative Learning in Biochemical Networks" J. Theor. Biol. 2007, 249, 58-66.

1999 – 2005

>> G. Ashkenasy, M.R. Ghadiri "Restructuring Artificial Peptide Networks by External Triggering", Biopolymers, 2005, 80, pp 587.
>> G. Ashkenasy, M.R. Ghadiri "Boolean Logic Functions of a Synthetic Peptide Network", J. Am. Chem. Soc. 2004, 126, 11140-11141.
* Citation: Chemistry World, Issue 10, Oct 2004.
>> G. Ashkenasy, R. Jagasia, M. Yadav, M.R. Ghadiri "Design of a Directed Molecular Network" Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 10872-10877.
>> G. Ashkenasy, R. Jagasia, M.R. Ghadiri "Emergence of Animate Behavior in Peptide-Based Ecosystems", Astrobiolgy, 2003, 2, 599.
>> G. Ashkenasy, D. Margulies, C.E. Felder, A. Shanzer, L.S. Powers "Bidentate Ligation of Heme Analogs; Novel Biomimetics of the Peroxidase Active Site", Chem. Eur. J. 2002, 8, 4017-4026.
>> G. Ashkenasy, D. Cahen, R. Cohen, A. Shanzer, A. Vilan, "Molecular Engineering of Semiconductor Surfaces and Devices" Acc. Chem. Res. 2002, 35, 121-128.
>> G. Ashkenasy, A. Ivanisevic, C.E. Felder, R. Cohen, D. Cahen, A.B. Ellis, A. Shanzer "Assemblies of ‘Hinged’ Iron-porphyrins as Potential Oxygen Sensors", J. Am. Chem. Soc. 2000, 122, 1116-1122.
* Citation: Anal. Chem. 2000, 72, 316A-317A.
>> DG. Wu#, G. Ashkenasy#, D. Shvarts, R.V. Ussyshkin, R. Naaman, A. Shanzer, D. Cahen "Novel NO Biosensor Based on Surface Derivatization of GaAs by ‘Hinged’ Ironporphyrins", Angew. Chem. Int. Ed. 2000, 39, 4496-4500.
#equal contribution;
* Citation: Anal. Chem. 2001, 73, 124A.
>> A. Ivanisevic, A.B. Ellis, G. Ashkenasy, A. Shanzer, Y. Rosenwaks "Linker-Enhanced Binding of Metalloporphyrins to Cadmium Selenide and Implications for Oxygen Detection", Langmuir, 2000, 16, 7852-7858.
>> G. Kalyuzhny, A. Vaskevich, G. Ashkenasy, A. Shanzer, I. Rubinstein, "UV/Vis Spectroscopy of Metalloporphyrin and Metallophthalocyanine Monolayers Self-Assembled on Ultrathin Gold Films", J. Phys. Chem. B, 2000, 104, 8238-8244.
>> G. Ashkenasy, G. Kalyuzhny, J. Libman, I. Rubinstein, A. Shanzer "Functional Monolayers With Coordinatively Embedded Metalloporphyrin Residues", Angew. Chem. Int. Ed. Engl. 1999, 38, 1257-1261.
>> A. Haran, R. Naaman, G. Ashkenasy, A. Shanzer, T. Quast, B. Winter, I.V. Hertel "Electron Transmission through Organized Organic Films Studied for Discrete Initial Electron Kinetic Energies", Eur. Phys. J. B, 1999, 8, 445-451.

Books and Book Chapters

>> R. Cohen, G. Ashkenasy, A. Shanzer, D. Cahen "Grafting Molecular Properties onto Semiconductor Surfaces" (2003) in Encycl. of Electrochem, vol. 6, pp. 127-152, Semiconductor electrodes & photoelectrochemistry, Editor S. Licht.
>> Z. Dadon, N. Wagner, R. Cohen-Luria, G. Ashkenasy "Reaction Networks" (2012) in Supramolecular Chemistry: From Molecules to Nanomaterials, vol 4, pp. 1527-1542, Editors P. Gale and J. Steed.
>> Z. Dadon, M. Samiappan, N. Wagner, N. Ashkenasy, G. Ashkenasy "Peptide Based Computation: Switches, Gates and Simple Arithmetic" (2012) in Biomolecular Information Processing: From Logic Systems to Sensors and Actuators, Editor E. Katz.
>> N. Wagner, Y. Raz, G. Ashkenasy "Theoretical Models of Generalized Quasispecies" (2015) in Quasispecies: From Theory to Experimental Systems, part of the series Current Topics in Microbiology and Immunology, pp1-19 , Editors E. Domingo and P. Schuster.