D. Jacobs: Scientific Publications (peer reviewed)
  • D. J. Jacobs and S. Dallakyan, Elucidating Protein Thermodynamics from the Three Dimensional Structure of the Native State Using Network Rigidity, Biophysical Journal in Press. (pdf)
  • D. R. Livesay, S. Dallakyan, G. G. Wood and D. J. Jacobs, A Flexible Approach for Understanding Protein Stability, FEBS Letters 576, 468-476 (2004). (pdf)
  • M. S. Lee, G. G. Wood and D. J. Jacobs, Investigations on the alpha-helix to coil transition in HP-heterogeneous polypeptides using network rigidity, J. Phys. Cond. Mat. 16, S5035-S5046 (2004) (Link)
  • B. M. Hespenheide, D. J. Jacobs and M. F. Thorpe, Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus. J. Phys. Cond. Mat. 16, S5055-S5064 (Link)
  • D. J. Jacobs and G. G. Wood, Understanding the a-Helix to Coil Transition in Polypeptides Using Network Rigidity: Predicting Heat and Cold Denaturation in Mixed Solvent Conditions Biopolymers, 75 1-31 (2004). (pdf)
  • D. J. Jacobs, S. Dallakyan, G. G. Wood and A. Heckathorne, Network rigidity at finite temperature: Relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems Physical Review E 68,  061109 (2003). (pdf)
  • D. J. Jacobs, A. Rader, L. A. Kuhn and M. F. Thorpe, Graph Theory Predictions of Protein Flexibility, Proteins: Structure, Function, and Genetics 44: no. 2, 150-155 (2001). (pdf)
  • M. F. Thorpe, A. Rader, M. Lei, D. J. Jacobs, L. A. Kuhn, Predicting Flexibility in Proteins using Constraint Theory, Journal of Molecular Graphics and Modeling 19, 60-69, (2001). (pdf)
  • M. F. Thorpe, D. J. Jacobs, M. V. Chubynsky and J. C. Phillips, Self organization in network glasses, J. Non-Crystalline Solids 266-269:859-866 (2000). (pdf)
  • P. M. Duxbury, D. J. Jacobs, M. F. Thorpe and C. Moukarzel, Floppy Modes and the Free Energy: Rigidity and Connectivity percolation on Bethe Lattices, Phys. Rev. E 59, 2084-2092 (1999). (pdf)
  • D. J. Jacobs, Generic Rigidity in Three-dimensional Bond-bending Networks, J. Phys. A Math. Gen. 31 6653-6668 (1998). (Link)
  • D. J. Jacobs and M. F. Thorpe, Comment on "Infinite-Cluster Geometry in Central-Force Networks", Phys. Rev. Lett. 80, no. 24, 5452 (1998). (pdf)
  • D. J. Jacobs and B. Hendrickson, An Algorithm for Two Dimensional Rigidity Percolation: The Pebble Game, J. Comput. Phys. 137, 346-365 (1997). (pdf)
  • D. J. Jacobs and M. F. Thorpe, Generic Rigidity Percolation: The Pebble Game, Phys. Rev. E 53, 3682-3693 (1996). (pdf)
  • D. J. Jacobs and M. F. Thorpe, Generic Rigidity: The Pebble Game, Phys. Rev. Lett. 75, 4051-4054 (1995). (pdf)
  • J. R. Dorfman, M. H. Ernst, R. Nix and D. J. Jacobs, Mean Field Theory for Lyapunov Exponents and Kolmogorov-Sinai Entropy in Lorentz Lattice Gases, Phys. Rev. Lett. 74, 4417-4410 (1995). (pdf)
  • J. R. Dorfman, M. H. Ernst and D. J. Jacobs, Dynamical Chaos in the Lorentz Lattice Gas, J. Stat. Phys. 81, 497-513 (1995).
  • S. Mukherjee, D. J. Jacobs and H. Nakanishi, Diffusion on Loopless Critical Percolation Cluster, J. Phys. A 28, 291-296 (1995). (Link)
  • D. J. Jacobs, S. Mukherjee and H. Nakanishi, Diffusion on DLA cluster in Two and Three Dimensions, J. Phys. A 27, 4341-4348 (1994). (Link)
  • D. J. Jacobs, and A. Masters, Domain Growth in a One-dimensional Diffusive Lattice Gas with Short Range Attraction, Phys. Rev. E 49, 2700-2710 (1994). (pdf)
  • D. J. Jacobs and H. Nakanishi, A Persistent Random Walk Model for the Frequency-Dependent Electrical Conductivity, Physica A 197, 204-222 (1993). (Link)
  • S. Muralidhar, D. J. Jacobs, D. Ramkrishna and H. Nakanishi, Diffusion on Percolation Clusters: Influence of Cluster Anisotropy, Phys. Rev. A 43, 6503-6517 (1991). (pdf)
  • S. Muralidhar, D. Ramkrishna, H. Nakanishi and D. J. Jacobs, Anomalous Diffusion: A Dynamic Perspective, Physica A 167, 539-553 (1990). (Link)
  • D. J. Jacobs and H. Nakanishi, Autocorrelation Functions for Discrete Random Walks on Disordered Lattice, Phys. Rev. A 41, 706-719 (1990). (pdf)
In Preparation
  • D. H. Huynh, S. Dallakyan and D.J. Jacobs, Connection Between Thermodynamics and Flexibility in Bacterial Periplasmic Binding Proteins. to be submitted to Journal of Molecular Biology.
  • D. Karabay, S. Dallakyan and D.J. Jacobs, N-H···O=C Hydrogen Bond Thermodynamics from a Single Particle Quantum Mechanical Model. to be submitted to J. Amer. Chem. Soc.
Proceedings and Chapters in Books
  • M. Chubynsky, B. Hespenheide, D.J. Jacobs, L.A. Kuhn, M. Lei, S. Menor, A.J. Rader, M.F. Thorpe, W. Whiteley and M.I. Zavodszky, Constraint Theory Applied to Proteins. To be published in the proceedings of the Indo-US Biopolymer workshop by Nova Publishers (2004). (pdf)
  • M. F. Thorpe, M. Chubynsky, B. Hespenheide, S. Menor, D.J. Jacobs, L.A. Kuhn, M.I. Zavodsky, M. Lei, A.J. Rader and W. Whiteley, Flexibility in Biomolecules. To be published as an article in the Sir Roger Elliott Festschift to be published by Imperial College Press (London, 2005). (pdf)
  • D.J. Jacobs, Understanding Protein Stability and Flexibility Using Network Rigidity, Conference Proceedings of the Second International Conference on Multiscale Materials Modeling.  Editor: Nasr M. Ghoniem,  ISBN 0-9762064-1-2, Printed by Mechanical and Aerospace Engineering Department, UCLA  386-388 (2004). (pdf)
  • M. F. Thorpe, M. V. Chubynsky, D. J. Jacobs, J. C. Phillips, Non-Randomness in Network Glasses and Rigidity, Glass Physics and Chemistry, Proceedings of the International Conference: Thermodynamics and Chemical Structure of Melts and Glasses. Nauka/Interperiodica International Acad. Pub. Co. 27, no. 2, 160-167 (2001).
  • M. F. Thorpe, M. V. Chubynsky, D. J. Jacobs and J. C. Phillips, Rigidity and Flexibility in Network Glasses in Panellhnio Sunedrio Fusikhs Stereas Katastasews xv, ed. by Aristeidhz Zdetshz Praktika Patra, 171-181 (2000).
  • D. J. Jacobs, L. A. Kuhn and M. F. Thorpe, Flexible and Rigid Regions in Proteins, 357-384 Rigidity Theory and Applications, (1999). Eds: M.F. Thorpe and P.M. Duxbury, Plenum Publishing , NY. (pdf)
  • M. F. Thorpe, D. J. Jacobs, N. V. Chubynsky and A. J. Rader, Generic Rigidity of Network Glasses, 239-277 Rigidity Theory and Applications, (1999). Eds: M.F. Thorpe and P.M. Duxbury, Plenum Publishing, New York. (pdf)
  • M. F. Thorpe, D. J. Jacobs and B. R. Djordjevic, The Structure and Rigidity of Network Glasses, to be published as a chapter in Insulating and Semiconducting Glasses, editor: Punit Boolchand, World Scientific Publishing Co., Inc. (1998). (pdf)
  • M. F. Thorpe, B. R. Djordjevic and D. J. Jacobs, The Structure and Mechanical Properties of Networks, in Amorphous Insulators and Semiconductors. Eds: M. F. Thorpe and M. I. Mitkova [NATO ASI Series 3] High Technology - Vol. 23 Kluwer Academic Publishers, 289-328 (1997). (pdf)
  • M. F. Thorpe, D. J. Jacobs and B. R. Djordjevic "Generic Rigidity Percolation," Condensed Matter Theories, Vol. II. Edited by E. V. Ludena, P. Vashishta and R. F. Bishop (Nova Science Publishers, 401-424 (1996). (pdf)
Invited Talks at Scientific Meeting
  • D. J. Jacobs, Predicting Protein Stability Using Network Rigidity at Finite Temperatures, Second International Conference on Multiscale Materials Modeling (MMM-II), in focus session “Multiscale Modeling of Biomaterials” at UCLA, Los Angeles, CA in Oct. 11-15, (2004).
  • D. J. Jacobs, Protein Stability and Flexibility: Application to Network Rigidity Modeling Protein Flexibility and Motions, Workshop at Banff International Research Station for Mathematical Innovation and Discovery (BIRS), Banff Canada, (Jul. 17-22, 2004).
  • D. J. Jacobs, Network Rigidity at Finite Temperatures and Free Energy Landscapes, American Mathematical Society, Lawrenceville, NJ, in focus session: Geometry of Protein Modeling, (April 17-18, 2004).
  • D. J. Jacobs, Predicting Protein Stability from a Free Energy Decomposition,
    Mathematics and Computer Science Workshop: The Geometry of Modeling Proteins, Bellairs Research Institute of McGill University, Holetown, Barbados, West Indies (Jan. 16-23, 2004).
  • D. J. Jacobs, Generic rigidity of glasses and proteins, in session Mapping Materials problems to graph algorithms, SIAM Annual conference, Atlanta GA (May 1999).
  • D. J. Jacobs, Real-time protein domain evaluator and design tool, DIMACS - Combinatorial Clustering and Multi-domain protein structure analysis, Rutgers University, NJ (June 1998).
  • D. J. Jacobs, Identifying floppy and rigid regions in proteins, Fundamental materials research series: Rigidity theory and Applications, Traverse City, MI (June 1998).
  • D. J. Jacobs, Graph rigidity: Applications to material science and proteins, Canadian Mathematical Society, Kingston, Ontario (Dec 1998).
Contributed Talks at Scientific Meeting ( Presenter is in red; CSUN students in bold)
  • Poster: Donald J. Jacobs, Sargis Dallakyan, Gregory Wood and Dennis R. Livesay. Protein Thermodynamics from the 3D topological structure of the Native State. 18th Symposium of the Protein Society, San Diego, CA  (Aug. 14-18, 2004).
  • Poster: Donald J. Jacobs, Sargis Dallakyan, Gregory Wood and Dennis R. Livesay. Protein Thermodynamics from the 3D topological structure of the Native State. Biopolymers Gordon Research Conference, Salve Regina University, Newport, RI  (June 13-18 2004).
  • Poster: Dundar Karabay, Sargis Dallakyan and Donald J. Jacobs.  Enthalpies and entropies for hydrogen bonds in proteins from quantum mechanics. 48th Biophysical Society Annual Meeting, Baltimore, MD (Feb 14-18, 2004).
  • Poster: Donald J. Jacobs, Sargis Dallakyan, Gregory Wood and Dennis R. Livesay. Protein Thermodynamics from the 3D topological structure of the Native State. 48th Biophysical Society Annual Meeting, Baltimore, MD Feb 14-18, (2004).
  • Talk: Gregory Wood, Sargis Dallakyan and Donald J. Jacobs. Protein Thermodynamics from the 3D Topological Structure of the Native State, American Physical Society, Annual March Meeting, Montreal, Quebec Canada (March 22-26, 2004).
  • Poster: Gregory Wood, Alicia Heckathorne and Donald J. Jacobs.  Network Rigidity Calculations of Cold Denaturation, American Physical Society, Annual March Meeting, Montreal Quebec, Canada  (March 22-26, (2004).
  • Talk: M. V. Chubynsky, M. F.  Thorpe, D. J. Jacobs and W. Whiteley, Rigidity of central-force elastic networks in three dimensions, American Physical Society, Annual March Meeting, Austin Convention Center; Austin, TX (March 3-7, 2003).
  • Poster: Alicia Heckathorne, Greg Wood and Donald J. Jacobs, Understanding folding and stability from a mechanical point of view: The alpha-helix to coil transition revisited. 47th Biophysical Society Annual Meeting, San Antonio, Texas (March 1-5, 2003).
  • Poster: Alicia Heckathorne and Donald J. Jacobs, The Alpha Helix to Coil Transition Revisited,Biopolymers. Gordon Research Conference, Salve Regina University, Newport RI, (June 16-21, 2002).
  • Poster: Dang H. Huynh, Jaime D. Osorio, Laura I. Gomez, Arnulfo Martinez, and D. J. Jacobs, Comparison of Conformational Flexibility in Four Homologous Periplasmic Binding Proteins. Biophysical Society annual meeting. San Francisco, CA (Feb 23-27, 2002).
  • Poster: (award winning) Dang H. Huynh, Jaime D. Osorio, Laura I. Gomez, Arnulfo Martinez, and D. J. Jacobs, Comparison of Conformational Flexibility in Four Homologous Periplasmic Binding Proteins. SACNAS (Society for Advancement of Chicanos and Native Americans in Science) National Conference, Phoenix Arizona, (September 27-30, 2001).
  • Poster: D. J. Jacobs and Jeremy Hules, Characterization of Conformational Flexibility in Hinge-Binding Proteins: Hierarchical Flexibility Maps in Terms of Dihedral Angle Internal Coordinates. Workshop on Protein Flexibility and Folding, Traverse City, Michigan (Aug 2000).
  • Poster: D. J. Jacobs, Characterizing the Degree of Flexibility in Proteins, Quantitative Challenges in the Post-Genomic Sequence Era. A workshop and symposium. San Diego, CA (Jan 2000).
  • Talk: D. J. Jacobs, L. A. Kuhn and M. F. Thorpe, Predicting conformational flexibility in protein structure, American Physical Society, Ohio section, Flint MI (May 1999).
  • Talk: D. J. Jacobs, L. A. Kuhn, and M. F. Thorpe, Flexibility and rigidity in protein structures, American Physical Society, Centennial meeting, Atlanta GA (Mar 1999).
  • Talk: D. J. Jacobs, M. F. Thorpe and L. A. Kuhn, Identifying floppy and rigid regions in proteins, Americian Physical Society, Los Angeles, CA (March 1998).
  • Poster: (award winning) D. J. Jacobs and M. F. Thorpe, Rigidity in network glasses and proteins, Center for fundamental materials research, Michigan State University. MI (April 1998).
Invited Seminars/Colloquium (as CSUN faculty)

Predicting Protein Stability from a Free Energy Decomposition
  • Physics and Astronomy Colloquium, CSUN Nov 12, 2003.
  • Biophysics Seminar, Physics Department, Arizona State University. March 4, 2004.
  • Computer Science Seminar, Rensselaer Polytechnic Institute. April 16, 2004.
  • Seminar, IRG Materials Research Lab UCSB, April 28, 2004.
  • Seminar, RISE-program, CSUN. June 28, 2004.
Understanding Protein Flexibility, Stability and Folding from a Mechanical Point of View
  • Physics and Astronomy Colloquium, CSUN. Feb 13, 2002.
  • Condensed Matter Seminar, Physics and Astronomy, UCLA. April 26, 2002.
  • Chemistry Department Colloquium, California State Polytechnic Univ., Pomona. May 7, 2002.
  • Chemical Engineering Department, Colorado State University. June 28, 2002.
  • Biophysics Seminar, Physics & Astronomy Department, Michigan State University, Aug 9 2002.
  • Seminar Series, Chemistry Department, University of California, Irvine. Sept 6, 2002.
  • Seminar Series, Department of Mechanical Engineering, Yale University, Dec 18, 2002
Conformational Flexibility in Protein Structure: Can it be Used Like a Fingerprint?
  • NASA-JPL PAIR program at CSUN. Oct 2, 2001.
Characterizing Conformational Flexibility in Proteins
  • Department of Chemical Engineering, Colorado State University. June 13, 2001.
  • Seminar, RISE-program, CSUN. June 29, 2001.
Characterizing Conformational Flexibility in Proteins with a FlexPrint: Working Toward a Finger Printing System
  • Graduate Student Seminar: Methods in Computational Biology Group, UCLA. July 11, 2000.

Generic Rigidity in Two and Three Dimensions and its Applications to Network Glasses and Protein Structure

  • Mathematical Physics Institute at CSUN. Sept 27, 1999.
Public Presentations
D. J. Jacobs, Analysis of Carey Hart's 360 degree mid-air vertical rotation on a motorcycle, Appeared on "Ripley's Believe It or Not" television show in Spring 2001.
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