Published Resources


This page is always under construction. For an updated publication list visit Dr. Kaznessis' Google Scholar profile at

PK Lai, YN Kaznessis, Free Energy Calculations of Microcin J25 Variants Binding to the FhuA Receptor, Journal of Chemical Theory and Computation, 2017, 13 (7), pp  3413–3423, DOI: 10.1021/acs.jctc.7b00417


PH Constantino, YN Kaznessis, Maximum Entropy Prediction of Non-Equilibrium Stationary Distributions for Stochastic Reaction Networks with Oscillatory Dynamics. Chemical Engineering Science, 2017,171, pp 139–148


K Geldart, YN Kaznessis, Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium, Antimicrob. Agents Chemother. April 2017 vol. 61 no. 4 e02033-16, doi: 10.1128/AAC.02033-16


Forkus B, Ritter S, Vlysidis M, Geldart K, Kaznessis YN. Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts. Sci Rep. 2017 Jan 17;7:40695. doi: 10.1038/srep40695.


Geldart K, Forkus B, McChesney E, McCue M, Kaznessis YN. pMPES: A Modular Peptide Expression System for the Delivery of Antimicrobial Peptides to the Site of Gastrointestinal Infections Using Probiotics. Pharmaceuticals (Basel). 2016 Oct 5;9(4). pii: E60.


PH Constantino, M Vlysidis, P Smadbeck, YN Kaznessis Modeling stochasticity in biochemical reaction networks Journal of Physics D: Applied Physics 49 (9), 093001


Ekblad B, Kyriakou PK, Oppegård C, Nissen-Meyer J, Kaznessis YN, Kristiansen PE. Structure-Function Analysis of the Two-Peptide Bacteriocin Plantaricin EF. Biochemistry. 2016 Sep 13;55(36):5106-16. doi: 10.1021/acs.biochem.6b00588.


Sfyroera G., Ricklin D., Reiss E. S. Chen H., Wu E., Kaznessis Y.N. Ekdahl K.N, Nilsson B, Lambris, J.D. " Rare Loss-of Function in Complement C3 Provides Insight into Molecular and Pathophysiological Determinants of Complement Activity", J Immunol. 2015 Apr 1;194(7):3305-16. doi: 10.4049/jimmunol.1402781.


McClintock M. Kaznessis Y.N., Hackel B. J. " Enterocin A Mutants Identified by Saturation Mutagenesis Enhance Potency Towards Vancomycin-Resistant Enterococci", Biotechnology and Bioengineering, 2016, 113, 414-422.


Constantino P. H., Vlysidis, M., Smadbeck P.,Kaznessis YN " Modeling Stochasticiy in Biochemical Reaction Networks ", Journal of Physics D Aplied Physics, 2016, 49 093001,


Kyriakou, P. K., Ekblad, B., Kristiansen, P. E., & Kaznessis, Y. N. (2016). Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1858(4), 824-835.


Geldart K., Borrero J., Kaznessis YN " Chloride-Inducible Expression Vector for Delivery of Antimicrobial Peptides Targeting Antibiotic-Resistant Enterococcus faecium ", Applied and Environmental Microbiology Volume: 81 Issue: 11 Pages: 3889-3897 Published: JUN 2015 
DOI: 10.1128/AEM.00227-15.


Smadbeck P, Kaznessis YN " Chemical master equation closure for computer-aided synthetic biology", Methods in molecular biology (Clifton, N.J.) Volume: 1244 Pages: 179-91 Published: 2015. DOI: 10.1007/978-1-4939-1878-2_9. 


Smadbeck P, Kaznessis YN "On a theory of stability for nonlinear stochastic chemical reaction networks", Journal of Chemical Physics Volume: 142 Issue: 18 Published: MAY 14 2015 
DOI: 10.1063/1.4919834.


Smadbeck P, Kaznessis YN "Solution of chemical master equations for nonlinear stochastic reaction networks", Current Opinion in Chemical Engineering 5, 90-95, 2014.


DS Bolintineanu, K Volzing, V Vivcharuk, A Sayyed-Ahmad, P Srivastava, YN Kaznessis " Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator ", Journal of Chemical & Engineering Data, 2014, 59, 3167-3176.


T Afroz, K Biliouris, Y Kaznessis, CL Beisel " Bacterial sugar utilization gives rise to distinct single-cell behaviours ", ACS Synthetic Biology, 2014, 93, 1093-1103.


J Borrero, Y Chen, GM Dunny, YN Kaznessis " Modified lactic acid bacteria detect and inhibit multi-resistant enterococci ", ACS Synthetic Biology, 2014.


T Afroz, K Biliouris, KE Boykin, Y Kaznessis, CL Beisel " Trade-offs in engineering sugar utilization pathways for titratable control " ACS Synthetic Biology, 2014.


Smadbeck P, Kaznessis YN, "A Closure Scheme for Chemical Master Equations", Proc Natl Acad Sci U S A. 2013 Aug 27; 110(35): 14261-5 10.1073/pnas.1306481110.


Biliouris K, Weeding E, Kaznessis Y, "SynBioS Designer Modeling Suite", Encyclopedia of Molecular Cell Biology and Molecular Medicine, in press. 


Volzing K, Borrero J, Sadowsky M, Kaznessis YN, "Antimicrobial Peptides Targeting Gram-negative Pathogens, Produced and Delivered by Lactic Acid Bacteria." ACS Synth Biol 2013 10.1021/sb4000367.


Smadbeck P, Kaznessis YN, "Efficient Moment Matrix Generation for Arbitrary Chemical Networks", Chem Eng Sci 2012, 84: 612-618 10.1016/j.ces.2012.08.031.


Smadbeck P, Kaznessis YN, "Stochastic Model Reduction Using a Modified Hill-type Kinetic Rate Law", J. Chem. Phys. 2012 137(23) 10.1063/1.4770273.


Bolintineanu D, Vivcharuk V, Kaznessis YN, "Multiscale Models of the Antimicrobial Peptide Protegrin-1 on Gram-Negative Bacteria Membranes", Int. J. Mol. Sci. 2012 13(9): 11000-11, 10.3390/ijms130911000.


Biliouris K, Babson D, Schmidt-Dannert C, Kaznessis YN. "Stochastic Simulations of a Synthetic Bacteria-Yeast Ecosystem" BMC Systems Biology, 2012; 6(58): 10.1186/1752-0509-6-58.


Volzing K, Biliouris K, Kaznessis YN. "proTeOn and proTeOff, New Protein Devices That Inducibly Activate Bacterial Gene Expression." ACS Chem Biol. 2011 Oct 21;6(10):1107-16.


Sotiropoulos V, Kaznessis YN., "Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics." Chem Eng Sci. 2011 Feb 1;66(3):268-277.


Kaznessis Y, "Mathematical models in biology: from molecules to life." Wiley Interdiscip Rev Syst Biol Med. 2011 May-Jun;3(3):314-22. doi: 10.1002/wsbm.142.


Bolintineanu D, Kaznessis YN. "Computational studies of protegrin antimicrobial peptides: a review." Peptides. 2011 Jan;32(1):188-201.


Vivcharuk V, Kaznessis YN. "Thermodynamic Analysis of Protegrin-1 Insertion and Permeation through a Lipid Bilayer." J Phys Chem B. 2011 Nov 1.


Chatterjee A, Drews L, Mehra S, Takano E, Kaznessis YN, Hu WS. "Convergent transcription in the butyrolactone regulon in Streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis." PLoS One. 2011;6(7):e21974.


Chatterjee A, Johnson CM, Shu CC, Kaznessis YN, Ramkrishna D, Dunny GM, Hu WS. "Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation." Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9721-6.


Biliouris K, Daoutidis P, Kaznessis YN. "Stochastic simulations of the tetracycline operon", BMC Syst Biol. 2011 Jan 19;5(1):9.


Qu H, Magotti P, Ricklin D, Wu EL, Kourtzelis I, Wu YQ, Kaznessis YN, Lambris JD. "Novel analogues of the therapeutic complement inhibitor compstatin with significantly improved affinity and potency." Mol Immunol . 2011 Jan;48(4):481-9.


Vivcharuk V, Kaznessis YN."Dimerization of protegrin-1 in different environments.", Int J Mol Sci . 2010 Sep 9;11(9):3177-9.


Weeding E, Houle J, Kaznessis YN SynBioSS Designer: A Web-Based Tool for the Automated Generation of Kinetic Models for Synthetic Biological ConstructsBriefings in Bioinformatics, 2010, 4:394-402.


Bolintineanu D, Hazrati E, Davis HT, Lehrer RI, Kaznessis YN. Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli. Peptides. 2010, 31(1):1-8.


Vivcharuk V, Kaznessis YN, Energy Profile of the Interaction between a Monomer or a Dimer of Protegrin-1 in a Specific Binding Orientation and a Model Lipid Bilayer, Journal of Physical Chemistry B, 2010.


Sayyed-Ahmad A, Kaznessis YN. Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model. PLoS One. 2009;4(3):e4799.


Kaznessis YN. "Multiscale models for synthetic biology." Conf Proc IEEE Eng Med Biol Soc. 2009;1:6408-11.


Langham A, Kaznessis YN. Molecular simulations of antimicrobial peptides. Methods Mol Biol. 2010;618:267-85.


Kaznessis YN. "Methods in Computational Synthetic Biology", Biotechnology Journal, 2009, 4(10):1392-1405.


Sayyed-Ahmad, A, Khandelia, H, Kaznessis YN. "Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles", Molecular Simulation, 2009, 35(10–11):986–997.


Ramalingam, KI, Tomshine, JR, Maynard, JA, Kaznessis YN. " Forward engineering of synthetic bio-logical AND gates" Biochemical Engineering Journal, 2009, 47(1-3):38-47.


Magotti P, Ricklin D, Qu H, Wu YQ, Kaznessis YN, Lambris JD. " Structure-kinetic relationship analysis of the therapeutic complement inhibitor compstatin " J Mol Recognit . 2009, 22(6):495-505.


Mulakala, C; Kaznessis YN "Path-Integral Method for Predicting Relative
Binding Affinities of Protein-Ligand Complexes" Journal of American Chemical Society, 2009 , 131 (12), 45214528.


Bolintineanu, D; Sayyed-Ahmad A; Davis HT; Kaznessis YN "Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore", PLoS Computational Biology, 2009, 5(1): e1000277.


Sotiropoulos, V.; Contou-Carrere, M-N; Daoutidis, P; Kaznessis YN "Model Reduction of Multiscale Chemical Langevin Equations: A Numerical Case Study" IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):470-82.


Sayyed-Ahmad, A.; Kaznessis, YN "Determining the Orientation of Protegrin-1 in DLPC Bilayers Using an Implicit Solvent-Membrane Model" PLoS One . 2009;4(3):e4799.


Chatterjee, A. Kaznessis Y., Hu, W-S. "Tweaking biological switches through a better understanding of bistability behavior" Current Opinion in Biotechnology, 2008, 19:475–481.


Chiu, T-L; Mulakala, C; Lambris, JD; Kaznessis, YN "Development of a New Pharmacophore Model That Discriminates Active Compstatin Analogs" Chem Biol Drug Des 2008; 72: 249–256


A. Hill, J. Tomshine, E. Wedding, V. Sotiropoulos, Y. Kaznessis, "SynBioSS: the Synthetic Biology Modeling Suite", Bioinformatics, 2008, 24(21):2551-2553


A. Langham, H. Khandelia, B. Schuster, A. Waring, R. Lehrer, Y. Kaznessis "Correlation between simulated physicochemical properties and hemolycity of protegrin-like antimicrobial peptides: Predicting experimental toxicity" Peptides, 2008, 29(7): 1085-1093. 


A. Langham, A. Sayyed-Ahmad, Y Kaznessis "On the nature of antimicrobial activity: A model for protegrin-1 pores", Journal of the American Chemical Society, 2008, 130(13): 4338-4346


Kaznessis YN. "Models for synthetic biology." BMC Systems Biology 2007 Nov 6;1(1):47


V. Sotiropoulos, YN. Kaznessis "An Adaptive Time Step Scheme for a System of SDE’s with Multiple Multiplicative Noise. Chemical Langevin Equation, a proof of concept", J. Chem. Phys. 2008, 128(1): 014103. 


Reddy BV, Kaznessis YN. "Use of secondary structural information and C alpha-C alpha distance restraints to model protein structures with MODELLER." Journal of Biosciences 2007 Aug;32(5):929-36.


D. Bolintineanu, A. Langham, T.H. Davis, Y. Kaznessis, "Molecular dynamics simulations of three protegrin-type anti-microbial peptides: interplay between charges at the termini, beta-sheet structure and amphiphilic interactions", Molecular Simulation, 2007, 33(9-10):809-819. 


A. Langham, A.J. Waring, Y. Kaznessis, "Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data", BMC Biochemistry. 2007 Jul 16;8(1):11. 


S. Vicatos, Y. Kaznessis, "Separating true positive predicted residue contacts from false positive ones in mainly alpha proteins, using constrained Metropolis MC simulations." Proteins, 2008, 70(2): 539-552. 


C. Mulakala, J.D. Lambris, Y. Kaznessis, "A simple, yet highly accurate, QSAR model captures the complement inhibitory activity of compstatin", Bioorg Med Chem. 2007 Feb 15;15(4):1638-44


H. Khandelia, Y. Kaznessis, "Structure of the Antimicrobial beta-hairpin Peptide Protegrin-1 in a DLPC Lipid Bilayer Investigated by Molecular Dynamics Simulation", BBA Biomembranes, 2007, 1768(3):509-20


H. Khandelia, Y. Kaznessis, "Cation-π Interactions Stabilize the Structure of the Antimicrobial Peptide Indolicidin near Membranes: Molecular Dynamics Simulations", J. Phys. Chem. B, 2007, 111(1):242-250


V. Sotiropoulos, Y. Kaznessis, "Computer-aided design of synthetic tetracycline-inducible regulatory networks", BMC Systems Biology, 2007, 1:7


H. Salis, Y. Kaznessis, "Using scaffold proteins to design gene-activating binary and ternary biological AND gates", 2006, 3(4):295-310, Physical Biology


A. Langham, Y. Kaznessis "Effects of mutations on the C-terminus of protegrin-1: a molecular dynamics simulation study", Molecular Simulation, 2006, 32(3-4):193-201. 


J. Tomshine, Y. Kaznessis, "Optimization of a stochastically-simulated gene network model via simulated annealing." Biophysical Journal, 2006, 91(9):3196-205


W. Wang, C. Mulakala, S.C. Ward, G. Jung, H. Luong, D. Pham , A.J. Waring, Y. Kaznessis, W. Lu, K.A. Bradley, R.I. Lehrer. "Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin." Journal of Biological Chemistry, 2006, 281(43):32755-64. 


H. Khandelia, A.Langham, Y. Kaznessis, "Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions", BBA, 2006, 1758(9):1224-34


Y. Duan, B. Reddy, Y. Kaznessis "Residue conservation information for generating near-native structures in protein-protein docking" Journal of Bioinformatics and Computational Biology, 2006, 4:793-806


H. Khandelia, Y. Kaznessis, "Molecular Dynamics Investigation of the Influence of Anionic and Zwitterionic Interfaces on Antimicrobial Peptides' Structure: Implications on Peptide Toxicity and Activity" Peptides, 2006, 27(6):1192-1200


H. Salis, V. Sotiropoulos, Y. Kaznessis, "Multiscale Hy3S: Hybrid stochastic simulation for supercomputers" BMC Bioinformatics, 2006, 7:93.


H. Salis, Y. Kaznessis, "An equation-free probabilistic steady state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks" Journal of Chemical Physical, 2005, 123 (21): Art. No. 214106.


L. Tuttle, H. Salis, J. Tomshine, Y. Kaznessis, "Model-driven design principles of gene networks: the oscillator" Biophysical Journal, 2005, 89 (6): 3873-3883.


A. Langham, H. Khandelia, Y. Kaznessis, "How can protegrin-1 be both a potent antimicrobial and harmfully toxic?: Molecular dynamics simulations of a beta-sheet antimicrobial peptide in micelles" Biopolymers: Peptide Science, 2006, 84 (2): 219-231.


Y. Kaznessis, “Multi-scale models for gene network engineering” Chemical Engineering Science, 2006, 61 (3): 940-953.


Y. Kaznessis, "A review of methods in computational prediction of blood-brain partitioning" Current Medicinal Chemistry, Central Nervous System Agents, 2005, 5, (3): 185-191


H. Khandelia, Y. Kaznessis, "Molecular dynamics simulations of helical antimicrobial peptides in SDS micelles: What do point mutations achieve?" Peptides, 2005, 26 (11): 2037-2049


V. Reddy, Y. Kaznessis, "Quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes" Journal of Bioinformatics and Computational Biology, 2005, 3(5):1137-50. 


H. Khandelia, Y. Kaznessis, "Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in zwitterionic dodecylphoshocholine micelles: Insights into host-cell toxicity" Journal of Physical Chemistry B, 2005; 109(26) pp 12990 - 12996 


Y. Duan, V. Reddy, Y. Kaznessis, "Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions" Protein Science, 2005 Feb; 14 (2): 316-328.


H. Salis, Y. Kaznessis, "Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions" Journal of Chemical Physics, 122, 054103 (2005).


H. Salis, Y. Kaznessis, "Numerical simulation of stochastic gene circuits" Computers & Chemical Engineering, Vol 29(3), 2005, p. 577-588.


S. Vicatos, V.B. Reddy, Y. Kaznessis, "Prediction of distant residue contacts with the use of evolutionary information" Proteins, Bioinformatics, Structure and Genetics, 2005 Mar 1; 58 (4): 935-49. 


A. Langham, Y. Kaznessis, "Molecular dynamics simulations of the N-terminus of HIV GP-41 fusion peptide in SDS micelles" Journal of Peptide Science, 2005 Feb; 14( 2): 316-328. 


N. Ostberg , H. Khandelia, Y. Kaznessis, “Protegrin structure activity relationships: Using homology models of synthetic sequences to determine structural characteristics important for activity” Peptides, Vol. 26(2), p. 297-306, 2005. 


H. Wei, Y. Kaznessis, ‘Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination” Biotechnology and Bioengineering, Vol. 89(1), p. 52-77, 2005. 


L.M. Gordon, P.W. Mobley, W. Lee, S. Eskandari, Y. Kaznessis, M.A. Sherman, A.J. Waring, "Conformational mapping of the N-terminal peptide of HIV-1 GP41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy" Protein Science, Vol. 13, p. 1012-30, 2004. 


Y. N. Kaznessis, R.G. Larson, “Molecular mechanics simulations and bioinformatics calculations in the study of lung surfactants.” Invited chapter in the book “Recent Research Developments in Lung Surfactant and its Dysfunction” Edited by Kaushik Nag, Marcel-Dekker, 2005 


Y. N. Kaznessis, S. Kim, R. G. Larson, “Specific mode of interaction between components of model pulmonary surfactants using computer simulations” Journal of Molecular Biology. Vol. 322, p. 569-582, 2002. 


Y. N. Kaznessis, S. Kim, R. G. Larson, “Simulations of zwitterionic and anionic phospholipid monolayers” Biophysical Journal, Vol. 82, 2002, p. 1731-42. 


Y. N. Kaznessis, M. E. Snow, C. J. Blankley, “Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water” Vol. 15, p. 697, 2001, Journal of Computer-Aided Molecular Design. 


Y. N. Kaznessis, L. Narashimhan, M. E. Snow, “Binding free energy calculations for Benzamidine-Trypsin complexes” Proceedings of Foundations of Molecular Modeling and Simulation Conference, AIChE Symposium Series, p. 283, 2000. 


Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “Dielectric relaxation of concentrated polymer solutions via molecular dynamics simulations” Journal of Chemical Physics, Vol. 111, p. 1325, 1999. 


Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “Concentration and size dependence of dielectric strength and dielectric relaxation of flexible polymers in dilute and semidilute solutions of a theta solvent” Macromolecules, Vol. 32, p. 1284, 1999. 


Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “Dielectric relaxation of dipole-inverted macromolecules using computer simulations” Macromolecules, Vol. 32, p. 6679, 1999. 


Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “A molecular dynamics study of macromolecules in good solvents. Comparison with dielectric spectroscopy experiments” Journal of Chemical Physics, Vol. 109, p. 5078, 1998. 


Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “Molecular dynamics simulations of polar polymer brushes" Macromolecules, Vol. 31, p. 3116, 1998.