Curriculum Vitae

Alkan Kabakçıoğlu
Department of Physics, Faculty of Arts and Sciences
Koç University
Rumelifeneri Yolu, Sariyer 34450, Istanbul
Turkey
e-mail: akabakcioglu [at] ku.edu.tr
Tel: +90-212-338-1830

EMPLOYMENT AND EDUCATION

Associate Professor at Koç University, Department of Physics,
Istanbul, Turkey 2016-present.

Assistant Professor at Koç University, Department of Physics,
Istanbul, Turkey Jan 2005-present.

Postdoctoral fellow at the University of Padova, Department of Physics,
Padova, Italy 2002-2004.

Design Scientist in InQuira.com,
Los Angeles, CA, 2000-2002

Dr. G. Picard Postdoctoral fellow at the Weizmann Institute of Science, Physics of Complex Systems,
Rehovot, Israel, 1999-2000.

PhD in Physics, MIT, Cambridge, Massachusetts,1993-1999.
Thesis title: `` Scaling Studies of Random-Field Tricriticality, Electronic Conduction Models,
and Interface Delocalization''
Thesis supervisor: Prof. A. Nihat Berker

MSc in Physics, Bilkent University, Ankara, Turkey,1990-1993.
Thesis title: ``Phase Transitions in Anisotropic Tetrahedral Ising Lattice: a Model for SiGe''
Thesis supervisor : Prof. M. Cemal Yalabık

BSc in Electrical Engineering, Bilkent University, Ankara, Turkey,1986-1990.
Thesis title: ``A New Algorithm for Real-Time Monitoring of ECG Signals''
Thesis supervisor: Prof. Ergin Atalar

WORK EXPERIENCE

R&D on natural-language processing (NLP):

• Unsupervised word sense selection algorithm design
• Automated ontology development from statistical analysis of large corpora

TEACHING EXPERIENCE

• Undergraduate courses taught at Koç University:
  
  ``MATH-101: Finite Mathematics''
  ``SCIE-109: Physics of Everyday Life''
  ``SCIE-111: Balance Sheet for Sustainable Energy''
  ``PHYS-101: General Physics I: Mechanics''
  ``PHYS-102: General Physics II: Electromagnetism''
  ``PHYS-205: General Physics III: Waves/Acoustics, Thermodynamics''
  ``PHYS-301: Statistical Physics''
  ``PHYS-403: Solid State Physics''
  ``CHEM-460/MASE-560: Statistical Thermodynamics''
  
  
• Graduate courses taught at Koç University:
  
  ``MATH-503: Applied Mathematics''
  ``MATH-506: Numerical Methods II''
  ``PHYS-501: Classical Mechanics''
  ``PHYS-506: Quantum Statistical Mechanics''
  ``PHYS-580: Selected Topics in Biological Physics''
  
  
• Recitation instructor for the following graduate courses at MIT:
  
  ``8.333: Statistical Mechanics I''
  ``8.334: Statistical Mechanics II''
  
  
• Recitation instructor for the following intensive courses at MIT:
  
  ``Superconductivity''
  ``Neural Networks and Simulated Annealing''
  ``Phase Transitions and Renormalization-Group Theory''
  
  

Publications

NEUROD2 regulates Stim1 expression and store-operated calcium entry in cortical neurons, G. Guner, G. Guzelsoy, F.S. Işleyen, G.S. &Scedxil;ahin, C. Akkaya, E. Bayam, E.I. Kotan, A. Kabakçıoğlu and G. Ince-Dunn, eNeuro, 4(1), 0255 (2017).

Coherent organization in gene regulation: a study on six networks, Neşe Aral and A. Kabakçıoğlu, Physical Biology, 13, 026006 (2016).

Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode coupling, B. Kav, M. Öztürk, and A. Kabakçıoğlu, Proteins: Structure, Function, and Bioinformatics, 84, 655-665 (2016).

Genome-wide target analysis of NeuroD2 reveals new insights into regulation of cortical projection neuron identity, E. Bayam, G.S. Sahin, G. Guzelsoy, G. Guner, A. Kabakçıoğlu, G. Ince-Dunn, BMC Genetics, 16, 681 (2015).

Coherent regulation in yeast's cell cycle network, N. Aral, A. Kabakçıoğlu, Physical Biology 12, 036002 (2015).

Mode coupling points to functionally important residues in myosin II, O. Varol, D. Yuret, B. Erman, and A. Kabakçıoğlu, Proteins: Structure, Function, and Bioinformatics, 82(9), 1777 (2014).

Denaturation of circular DNA: supercoils and overtwist, A. Bar, A. Kabakçıoğlu, and D. Mukamel, Phys. Rev. E, 86(6), 061904 (2012).

Deep spin-glass hysteresis area collapse and scaling in the d=3 +/-J Ising model, O. Sarıyer, A. Kabakçıoğlu, and A. N. Berker, Phys. Rev. E, 86(4), 041107 (2012).

Constrained thermal denaturation of DNA under fixed linking number, A. Bar, A. Kabakçıoğlu, and D. Mukamel, CEJP, 10(3), 582 (2012).

Macroscopic loop formation in circular DNA denaturation, A. Kabakçıoğlu, A. Bar, and D. Mukamel, Phys. Rev. E, 85(5), 051919 (2012).

Denaturation of circular DNA: Supercoil mechanism, A. Bar, A. Kabakçıoğlu, and D. Mukamel, Phys. Rev. E, 84(4), 041935 (2011).

Twist/writhe partitioning in a coarse-grained DNA minicircle model, M. Sayar, B. Avsaroğlu, and A. Kabakçıoğlu, Phys. Rev. E, 81, 041916 (2010).

Anharmonicity and mode-coupling in a fluctuating native protein , A. Kabakçıoğlu, M. Gur, D. Yuret, and B. Erman, Physical Biology, 7, 046005 (2010).

New results on the melting thermodynamics of a circular DNA chain, A. Kabakçıoğlu, E. Orlandini, and D. Mukamel, Physica A,389 (15), 3002-3006 (2010). MIT Symposium article dedicated to A. Nihat Berker on his 60th Birthday.

Anomalies in the transcriptional regulatory network of Saccharomyces Cerevisiae, M. Tuğrul and A. Kabakçıoğlu, Journal of Theoretical Biology, 263 (3), 328-336 (2010).

Robustness of Transcriptional Regulation in Yeast-like Model Boolean Networks, M. Tuğrul and A. Kabakçıoğlu, Int. J. Bifur. Chaos, 20 (3), 929-935 (2010). "Modelling and Computation on Complex Networks", conference proceedings.

Supercoil formation in DNA denaturation, A. Kabakçıoğlu, E. Orlandini, and D. Mukamel, Phys. Rev. E 80 (1), 010903, Rapid Comm. (2009).

Transcriptional regulatory network topology from statistics of DNA binding sites, A. Kabakçıoğlu, Physica A 386, 764-769 (2007). Proceedings of the Pan American Scientific Institute (PASI) Conference on Disorder and Complexity.

Percolation transition in a dynamically clustered network, A. Zen, A. Kabakçıoğlu, and A.L. Stella, Phys. Rev. E 76, 026110 (2007).

The Information Coded in the Yeast Response Elements Accounts for Most of the Topological Properties of Its Transcriptional Regulation Network, D. Balcan, A. Kabakçıoğlu, M. Mungan, and A. Erzan, PLoS ONE 2(6): e501 (2007).

A scale free network hidden in the collapsing polymer, A. Kabakçıoğlu and A. L. Stella, Phys. Rev. E 72, 055102 (2005).

Analytical solution of a stochastic content-based network model, M. Mungan, A. Kabakçıoğlu, D. Balcan, and A. Erzan, J. Phys. A: Math. Gen. 38 9599 (2005).

Pseudoknots in a Homopolymer, A. Kabakçıoğlu and A. L. Stella, Phys. Rev. E 70, 011802 (2004). Also selected for publication in the August 1, 2004 issue of Virtual Journal of Biological Physics Research.

Connection-Length Optimization in Scale-Free Networks, S. S. Manna and A. Kabakçıoğlu, J. Phys. A: Math. Gen. 36, L279-L285 (2003).

Scaling Behavior of a Multiply Connected Fluctuating Interface in Two Dimensions,, H. Kaya, A. Kabakçıoğlu, and A. Erzan, Fractals 11 227-232 (2003).

Statistical Properties of Contact Vectors, A. Kabakçıoğlu, M. Vendruscolo, I. Kanter, and E. Domany, Phys. Rev. E 65, 41904 (2002).

Hard-Spin Mean-Field Theory: A Systematic Derivation and Exact Correlations in One Dimension, A. Kabakçıoğlu, Phys. Rev. E 61, 3366 (2000).

Delocalization Transition of a Rough Adsorption-Reaction Interface, H. Kaya, A. Kabakçıoğlu, and A. Erzan, Phys. Rev. E 61, 1102 (2000).

Strongly Asymmetric Tricriticality of Quenched Random-Field Systems, A. Kabakçıoğlu and A.N. Berker, Phys. Rev. Lett. 82, 2572 (1999).

Hard-Spin Mean-Field Theory, A.N. Berker, A. Kabakçıoğlu, R.R. Netz, and M.C. Yalabık, Tr. J. of Physics 18, 354 (1994).

Phase Transitions in Anisotropic Tetrahedral Ising Lattice, A. Kabakçıoğlu and M.C. Yalabık, Tr. J. of Physics 18, 404 (1994).

Closed-Form Solutions and Free Energy of Hard-Spin Mean-Field Theory of a Fully Frustrated System, A. Kabakçıoğlu, A.N. Berker, and M.C. Yalabık, Phys. Rev. E 49, 2680 (1993).

Grants

MFAG-114F348 Principle Investigator "Dynamical behavior of helical biomolecules and the influence of geometrical entanglement on scaling properties" (2015-2018).

114E053 Investigator "Composite network modelling for neuropsychologial disorders and its application to Alzheimer's disease" (2014-2017).

MFAG-113F092 Principle Investigator "A novel method for identifying the functionally critical regions in allosteric proteins, based on dynamical analysis of mode coupling" (2013-2016).

TBAG-110T618 Principle Investigator "Investigation of the effects of molecular geometry on the thermal denaturation of DNA" (2011-2013). Completed.

TBAG-106T553 Principle Investigator "Investigation of the transcriptional regulatory network of the Yeast" (2007-2010). Completed.

TBAG-108T553 Investigator "A coarse-grained model of DNA and investigation of the plasmid structure as a function of temperature" (2008-2011). Completed.

TUBITAK-BIDEB Grant for IARS Summer School on "Biopolymers and Bioinformatics" (July 2008).

TUBITAK-BIDEB Travel Grant for Guest Scientist Support Program (July 2008).

Presentations

Mimar Sinan Univ, Istanbul (Mar 12, 2015).

APS March Meeting, St Antonio TX, USA (Mar 2, 2015).

21st Statistical Physics Days, Erciyes University, Kayseri, Turkey (June 23, 2014).

Short talk, 7. Traditional International "Mirror Conference" on Statistical and Condensed Matter Physics, Minerva Palas, Sabanci Univ., Istanbul (Dec 23, 2013).

Biophysics Chalk Talk, MIT, Boston (May 7, 2013).

108th Statistical Mechanics Meeting, Rutgers University (16-18 Dec, 2012).

Bogazici Univ, Istanbul (Nov 14, 2012).

APS March Meeting, Boston MA, USA (Feb 27, 2012).

Middle East Technical Univ (ODTU), Ankara (Oct 26, 2011).

SigmaPhi-2011, Workshop on Biophysics, Cyprus (July 11-15, 2011).

Bilkent University, Dept. of Physics (Apr 13, 2011).

Short talk, Mirror Conference of the Dallas Meeting of APS, 103. Statistical Physics Conference, Feza Gursey Inst., Istanbul (Dec 2010).

Invited talk, 2nd Greek-Turkish Conference on Statistical Mechanics and Dynamical Systems (Sep 2010).

Catholic University of Leuven, Belgium (Jun 2010).

Padova University, Dept. of Physics (Apr 27, 2010).

Sabanci Univ., Istanbul (Mar 2010).

APS March Meeting, Portland OR, USA (Mar 16, 2010).

MIT, Prof. Nihat Berker's 60th Birthday Celebration Symposium (Oct 17, 2009).

Weizmann Institute of Science, Dept. of Physics of Complex Systems (May 25, 2009).

Bogazici University, Dept. of Physics (Mar 18, 2009).

100th Statistical Mechanics Meeting, Rutgers University (Dec 14-18, 2008).

invited talk at the Greek-Turkish Conference on Statistical Mechanics and Dynamical Systems, Rhodos-Greece (Sept 11-17, 2008).

Istanbul University, Kortel Seminar Series (Mar 27, 2008).

Scuola Superiore di Catania (Dec 19, 2007).

98th Statistical Mechanics Meeting, Rutgers University (Dec 16, 2007).

Invited talk at the meeting Stochastic Networks and Internet Technology at Scuola Normale Superiore, Pisa (Sept, 2007).

Invited talk at the annual meeting of Turkish Physical Society (August 21-24, 2007).

PASI conference on disordered and complex systems (2006).

Istanbul Technical University, 13th Statistical Physics Days (2006).

Bogazici University, Department of Physics (30 Nov, 2005).

94th Statistical Mechanics Meeting, Rutgers University (2005).

Invited talk in Istanbul Technical University 11th Statistical Physics Days (2004).

Invited talk in Bioinformatics Cluster-EURO/INFORMS 2003 Meeting, Koç Univesity (2003).

Invited talk in CECAM workshop on Statistical mechanics of random copolymers, Lyon (2003).

Invited talk in Istanbul Technical University 6th Statistical Physics Days (1999).

80th Statistical Mechanics Meeting, Rutgers University (1998).

79th Statistical Mechanics Meeting, Rutgers University (1998).

Istanbul Technical University 5th Statistical Physics Days (1998).

APS March Meeting, Pittsburgh (1994).

Istanbul Technical University 1st Statistical Physics Days (1994).

Schools / Workshops

• Invited lecture at the Joint Summer School of Feza Gursey Institute - Imperial College on Complex Systems, Istanbul Turkey (Sept 05-10, 2011).

• Associate Lecturer at the Summer School on "Augmented Physics", Feza Gursey Institute, Istanbul Turkey (Jul 12-23, 2009).

• Invited lecture series on ``Advanced Statistical Mechanics for Condensed Matter Physicists'' IARS, Turunc-Marmaris (Jul 5-18, 2009).

• Lecture on ``Thermal Denaturation of linear and plasmid DNA'', Summer School on "Augmented Physics", Feza Gursey Institute, Istanbul Turkey (Aug 27, 2008).

• Organizer of the International Advanced Research School (IARS) on "Biopolymers and Bioinformatics", Turunc-Marmaris, Turkey (7-18 July 2008).

• Lecturer and the organizing commitee member of the International Advanced Research School (IARS) on "Statistical Mechanics and Complexity", Turunc-Marmaris, Turkey (July 2007).

• Organizing commitee member and oral contribution at the "Workshop on New Directions in Complex Systems", Buyukada-Istanbul, Turkey (September 2006).

• Invited talk at the bilateral workshop on "Basics in Real-Space Theories" at Max Planck Institute, Dresden (July 17-19, 2006).

• Lectures at the summer school on "Numerical and Quasi-Numerical Methods in Solid-State Physics", Mugla, Turkey (June, 2005).