Publications

2009

Amy Bauer, Trachette Jackson, Yi Jiang and Thimo Rohlf, "Stochastic network model of receptor cross-talk explains pro- and anti-angiogenic control ", under review , 2009
Xin Zhou and Yi Jiang, "Fast Adaptive Flat-histogram Ensemble for Calculating Density of States and Enhanced Sampling in Large Systems ", under review, 2009
Kejing He, Yi Jiang and Shoubin Dong, "A Hybrid Parallel Framework for the Cellular Potts Model Simulations ", under review, 2009
Yilin Wu, Dale Kaiser, Yi Jiang and Mark Alber, "Periodic Reversal of Direction Allows Myxobacteria to Swarm", in press PNAS , 2009
Juan Restrepo, Rustum Choksi, James Hyman and Yi Jiang, "Improving the Damage Accumulation in a Biomechanical Bone Remodeling Model", in press Computer Methods in Biomechanical and Biomedical Engineering , 2009

2008

Ilya Nemenman, William Hlavacek, Jerremy Edwards, James Faeder, Yi Jiang and Michael Wall, " Editorial: Selected papers from the first q-bio conference on cellular information processing ", IET Systems Biology, vol. 2 , pp. 203-205, 2008
Pawel Weronski, Yi Jiang and Steen Rasmussen, "Application of free energy perturbation approach for calculating adsorption energy of small PNA molecules at lipid-water interface", Submitted to Biophysial Journal, 2008
Amy Bauer, Trachette Jackson and Yi Jiang, "Topography of Extracellular Matrix Mediates Vascular Morphogenesis and Migration Speeds ", Submitted to Biophysical Journal, 2008
Yi Jiang, Bryan Travis, Chad Knutson, Jinsuo Zhang and Pawel Weronski, "Numerical Methods for Protocell Simulations", Protocells:Bridging Nonliving and Living Matter, vol. , pp. 407-432, 2008
Pawel Weronski, Yi Jiang and Steen Rasmussen, "Application of Molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine", Complexity, vol. 13, pp. 10-17, 2008
Xin Zhou, Yi Jiang, Steen Rasmussen and Hans Ziock, "Bridging coarse-grained models by jump-in-sample simulation", Journal of Chemial Physics, vol. 128, pp. 174107-1-7, 2008

2007

Yilin Wu, Yi Jiang, Dale Kaiser and Mark Alber, "Type IV Pili Facilitate the Collective Motion of Bacteria: Modeling Myxobacterial Swarming", PLoS Computational Biology , vol. 3, pp. e253, 2007
Xin Zhou and Yi Jiang, "A general long-time molecular dynamics scheme in atomistic systems: Hyperdynamics in entropy dominated systems", Lecture Notes in Computer Science, vol. 4487, pp. 826--833, 2007
Jeremy Edwards, James Faeder, William Hlavacek, Yi Jiang, Ilya Nememan and Michael Wall, "Q-bio 2007: a watershed moment in modern biology", Molecular Systems Biology, vol. 3, pp. 148, 2007
Yi Jiang, "A multiscale, cell-based framework for modeling cancer development", Lecture Notes in Computer Sciences, vol. 4487, pp. 770--777, 2007
Amy Bauer, Trachette Jackson and Yi Jiang, "A Cell-Based Model Exhibiting Branching and Anastomosis During Tumor-Induced Angiogenesis", Biophysical Journal , vol. 92, pp. 3105--3121, 2007
Christophe Raufaste, Benjamin Dollet, Simon Cox, Francois Graner and Yi Jiang, "Yield drag in a two-dimensional foam flow around a circular obstacle: the role of fluid fraction", European Physical Journal E, vol. 23, pp. 217--228, 2007
Pawel Weronski, Yi Jiang and Steen Rasmussen, "Molecular Dynamics Studies of PNA Partitioning in Lipid Bilayers", Biophysical Journal , vol. 92, pp. 3081--3091, 2007

2006

Olga Sozinova, Yi Jiang, Dale Kaiser and Mark Alber, "A three-dimensional mdoel of myxobacterial fruiting body formation", Proceedings of National Academy of Sciences USA, vol. 103, pp. 17255--17259 , 2006
Yilin Wu, Nan Chen, Mathew Rissler, Yi Jiang, Dale Kaiser and Mark Alber, "CA Models of Myxobacterial Swarming", Lecture Notes in Computer Science, vol. 4173, pp. 192-203, 2006
Xin Zhou, Yi Jiang, Kurt Kramer, Steen Rasmussen and Hans Ziock, "Hyperdynamics for entropic systems: Time-space compression and pair correlation function approximation", Physical Review E Rapid Communication, vol. 74, pp. 035701(R), 2006
Yi Jiang, Olga Sozinova and Mark Alber, "The collective behaviors of Myxobacteria", Advances in Complex Systems, vol. 9, pp. 353--368, 2006
Yi Jiang, "Understanding a killer: A predictive model for tumor development", Contemporary Mathematics, vol. 410, pp. 173--185, 2006

2005

Olga Sozinova, Yi Jiang, Dale Kaiser and Mark Alber, "A Three-Dimensional Model of Myxobacterial Aggregation by Contact-mediated Interactions ", Proceedings of the National Academy of Science USA , vol. 102 , pp. 11308-11312, 2005
Yi Jiang, Jelena Pjesivac, Charles Cantrell and James Freyer, "A Multiscale Model for Avascular Tumor Growth ", Biophysical Journal , vol. 89, pp. 3873--3883, 2005
Jinsuo Zhang, Yi Jiang, Steen Rasmussen and Hans Ziock, "Lipid aggregation as a function of aggregation number", Preprint: LA-UR-05-5480, 2005

2004

Mark Alber, Maria A. Kiskowski and Yi Jiang, "Two-Stage Aggregate Formation via Streams in Myxobacteria", Physical Review Letters , vol. 93, pp. 068192, 2004
Maria A. Kiskowski, Yi Jiang and Mark Alber, "Role of streams in myxobacteria aggregate formation ", Physical Biology , vol. 1, pp. 173-183, 2004
Mark Alber, Maria Kiskowski and Yi Jiang, "Lattice Gas Cellular Automata Model For Rippling in Myxobacteria", Physica D , vol. 191, pp. 343 , 2004
Mark Alber, Maria Kiskowski, Yi Jiang and Stuart Newman, "Biological Lattice Gas Models", in Dynamics and Bifurcation of Patterns in Dissipative Systems, World Scientific Series on Nonlinear Science, Volume 12 , pp. 272-291, 2004

2003

Marius Asipauskas, Miguel Aubouy, James A. Glazier, Francois Graner and Yi Jiang, "A texture tensor to quantify deformations: the example of two-dimensional flowing foams ", Granular Matter, vol. 5, pp. 71-76, 2003
Miguel Aubouy, Yi Jiang, James A. Glazier and Francois Graner, "A texture tensor to quantify deformations", Granular Matter, vol. 5, pp. 64-70, 2003

2002

Mark Alber, Maria Kiskowski, James Glazier and Yi Jiang, "On Cellular Automaton Approaches to Modeling Biological Cells", in IMA 134: Mathematical systems theory in biology, communication, and finance. Springer-Verleg, New York. , pp. 12, 2002

2001

Francois Graner, Yi Jiang, Eric Janiaud and Cyril Flement, "Equilibrium states and ground state of 2D fluid foams", Phys. Rev. E, vol. 63, pp. 011402, 2001

2000

Yi Jiang, Marius Asipauskas, James Glazier and Francois Graner, " Ab Initio derivation of mesoscopic stress and stain in foams", in Foams, Emulsions and their Applications, P. Zitha, J. Banhart and G. Verbist editors (Verlag MIT Publishing, Bremen, Germany, 2000) , pp. 297-304, 2000
Yi Jiang, Turab Lookman and Avadh Saxena, "Influence of filler particles and cluster on phase-separating filled polymer blends", in MRS Proceedings:Filled and Nanocomposite Polymer Materials , pp. kk8.5.1-6, 2000
Yi Jiang, Turab Lookman and Avadh Saxena, "Phase Separation and Shape Deformation on a Two-Phase Membrane", Phys. Rev. E, vol. 61, pp. R57-R60, 2000
Yi Jiang, Eric Janiaud, Cyril Flament, James Glazier and Francois Graner, " Energy landscape of 2D fluid foams", in Foams, Emulsions and their Applications, P. Zitha, J. Banhart and G. Verbist editors (Verlag MIT Publishing, Bremen, Germany, 2000) , pp. 321-327, 2000

1999

Florence Elias , Cyril Flament , James Glazier , Francois Graner and Yi Jiang, " Foams Out of Stable Equilibrium: Cell Elongation and Side Swapping", Phil. Mag. B, vol. 79, pp. 729-751, 1999
Yi Jiang, Pieter Swart, Avadh Saxena, Marius Asipauskas and James Glazier, "Hysteresis and Avalanches in Two Dimensional Foam Rheology Simulations", Phys. Rev. E, vol. 59, pp. 5819-5832, 1999

1998

Yi Jiang, Herbert Levine and James Glazier, " Differential adhesion and chemotaxis in mound formtaion of Dictyostelium", Biophys. J., vol. 75, pp. 2615, 1998
Yi Jiang, Cellular Pattern Formation, PhD thesis, University of Notre Dame, 1998

1997

Yi Jiang and James Glazier, "Foam Drainage: Extended Large-Q Potts Model Simulation and a Mean Field Theory", in MRS Proceedings:MRS Fall Meeting'96: Volume 463 , pp. 307, 1997

1996

Yi Jiang and James Glazier, " Extended Large-Q Potts Model Simulation of Foam Drainage", Phil. Mag. Lett., vol. 74, pp. 119-128, 1996

1995

Yi Jiang, Jose C. M. Mombach and James Glazier, " Grain Growth From Homogeneous Initial Conditions: Anomalous Grain Growth and Special Scaling States", Phys. Rev. E, vol. 52, pp. R3333-36, 1995

1994

H. Weng, D. Wang, Yi Jiang and X. Liu, " Low Energy Positron Beam Studies of Nano-TiN Films", Mat. Sci. Eng. B, vol. 26, pp. 163, 1994

1992

D. Zhang, B. Yang and Yi Jiang, " Mossbauer Study of the High-Temperature BiPbSrCaCuSnO Superconductor", Solid State Comm., vol. 83, pp. 999, 1992