Homepage of Yilin Wu

Department of Physics University of Notre Dame   Mailing address: Yilin Wu Nieuwland Science Hall, 336 Notre Dame, IN 46556, USA Office Phone: (574) 631-6590 Email: ywu1 AT nd.edu, or wyilin AT gmail.com (Please change "AT" to "@")

  Education:

• 09/2004 - present,   Ph. D candidate in Physics, University of Notre Dame, Notre Dame, USA. (expected in 2009)
                                    Advisor: Mark Alber; Mentors: Yi Jiang (Los Alamos National Laboratory), Dale Kaiser (Stanford University)




• 09/2000 - 07/2004, B. S. in Physics, University of Science&Technology of China, Hefei, China.
                                    Advisor: Bing-Hong Wang

  Research Interest:

My general interest is to understand the physics of living systems, which guides me throughout the efforts to find out "how and why" of specific
biological systems. My PhD research has focused on understanding the physics of bacterial swarming and other collective biological phenomena
like vascular network formation. Working closely with biologists (and sometimes doing experiments on my own), I build stochastic (Monte Carlo)
and numerical models to solve the problems. For future research I have interests in exploring the following topics both theoretically and experimentally:




• Multi-cellular phenomena and pattern formation in biology.
  I like to find out how the population dynamics arise from the movement pattern, signaling and interactions of individual cells, and to understand
  why cells in a group behave in specific ways. In my work on bacterial swarming (Myxobacteria), I build computational models to tackle the
  problem how social interactions and the individual movement algorithm affects the swarming efficiency of colonies. It turns out bacterial cells are
  smart enough to coordinate their movements in dense conditions using some basic physics even though they have only simple sensory systems.
  




• The physics of cellular machinery and its link to thermodynamics.
  To me living system is the most amazing state of matter in the Universe. What drives the emergence, evolution and adaptation of life? As a step
  towards this question, I would like to study how cell machinery works and interacts, and how the stochasticity at molecular level is transformed to
  order and how intrinsic noise affects the functioning of cells.
  

  Peer-reviewed Publications:

[5]. Wu Y, Kaiser D, Jiang Y, Alber M (2009) (in preparation).




[4]. Wu Y, Kaiser D, Jiang Y, Alber M (2009) Periodic reversal allows Myxobacteria to swarm. Proc Natl Acad Sci USA 106(4): 1222–1227.
       Download PDF        Nature News article

      Abstract: During swarming, myxobacteria cells move back and forth periodcially. Why do they choose such an expansive
      way to invest energy? Our results give a plausible answer to this question from evolutionary point of view, and suggest a
      crucial component in the general behavioral algorithm governing bacterial swarming.

[3]. Wu Y, Jiang Y, Kaiser D, Alber M (2007) Social interactions in myxobacterial swarming. PLoS Comput Biol 3(12): e253.
      Open access


      Abstract: Myxobacteria have two motility mutants; one of them moves with type-IV pili. Our story begins with the fact that
      wild-type colonies swarm faster than the sum of both mutants, whereas individual cells of both mutants move at similar
      speeds as wild-type. How does this synergy at population-level happen? Our work suggests that it may be because of the
      local alignment effect of type-IV pili mediated motility.

[2]. Wu, Y.L., Chen, N., Rissler, M., Jiang, Y., Kaiser, D., and Alber, M. CA Models of Myxobacteria Swarming, S. El Yacoubi, B. Chopard,
      and S. Bandini (Eds.): ACRI 2006, LNCS 4173, Springer-Verlag Berlin Heidelberg, pp. 192-203, 2006.


      Abstract: Two models as well as their potential for studying collective motion of bacteria are introduced.

[1]. Yang WS, Wang BH, Wu YL, Xie YB. Searching good strategies in evolutionary minority game using variable length genetic algorithm.
      Physica A, 339 (2004) 583-590.

  Presentations and Conferences:

- The Second Q-bio Conference, Sante Fe, 2008 (with travel award).


 Spotlight talk: A Computational Model for Bacterial Swarming

- The 35th Annual International Conference on the Biology of Myxobacteria, Napa Valley, 2008.


 Talk title: Why Myxococcus Reverses?

- T-7/CNLS Student Talk, Center for Nonlinear Studies (CNLS), Los Alamos National Lab, July 2008.


 Talk Title: Periodic reversals allow bacteria to swarm

- Workshop on Interdisciplinary Biomedical Research, University of Notre Dame and Indiana University School of Medicine, 2008.


 Talk Title: Role of Type IV Pili-mediated Motility in the Collective motion of Bacteria

- Microfluids workshop, Mathematical Biosciences Institute, OSU. 2007.

- The First Q-bio Summer School and Conference hosted by CNLS, Los Alamos National Laboratory, Sante Fe, 2007 (with scholarship)

- T-7/CNLS Student Talk, Center for Nonlinear Studies (CNLS), Los Alamos National Lab, August 2007.


 Talk Title: Blood-vessel network formation in early stage of embryo development

- Poster presentation at CNLS Annual Conference: Complexity of Biological and Soft Materials (LANL), Santa Fe, New Mexico. 2007
    (with travel award)

- Poster presentation at APS March meeting, Denver, CO, 2007.

- Poster presentation at LANL Student Symposium, Los Alamos National Laboratory, 2006.

  Professional Experience:

Research




08/2005 - present, Center for the Study of Biocomplexity, University of Notre Dame. Project: Model the swarming and aggregation of
Myxobacteria.




09/2008 - present, Department of Civil Engineering ( Prof. Joshua Shrout's lab), University of Notre Dame. Project: Study the swarming
dynamics of social motility mutant of Myxococcus xanthus.




06/2008 – 08/2008, Graduate Research Assistant, Group T-7/Mathematical Modeling and Analysis and Center for Nonlinear Studies (CNLS),
Los Alamos National Lab. Project: Understand the traffic control in bacterial swarming.




05/2007 – 08/2007, Student Visitor, Group T-7/Mathematical Modeling and Analysis, Los Alamos National Lab. Project: Model the vascular
network formation in early embryo development and study the virus spreading in lung epithelial tissue.




10/2006 – 05/2007, Department of Chemistry and Biochemistry ( Prof. Holly Goodson’s lab), University of Notre Dame. Project: Culture
Myxobacteria (Myxococcus xanthus) and image the movement pattern of cells.




05/2006 – 08/2006, Student Visitor, Group T-7/Mathematical Modeling and Analysis, Los Alamos National Lab. Project: Understand the
role of type-IV pili in the collective motion of Myxobacteria.




07/2003 – 06/2004, Center of Nonlinear Science, USTC (China). Project: Study the collective behavior of adaptive complex systems.




Teaching




08/2004 - 05/2006. Teaching Assistant, Department of Physics, University of Notre Dame.

  Skills and Techniques:

- Operating systems: Windows, Linux, Macintosh




- Coding Languages: C/C++, Fortran




- Scientific tools: Mathematica, Matlab, Origin




- Tex formatting: LaTeX, Word, Excel, PowerPoint.

  Fun activities:

• Jogging is my favorite exercise. It not only brings me fresh air but also fresh ideas. I enjoy hiking as well, especially in mountains.

• I like folk art, and worked twice as an artist assistant in Santa Fe International Folk Art Market (2006 and 2007).

• I used to practise Sino-calligraphy and Shan-shui painting...long time ago.

Last modified:   11/09/2008