Theory and Computation of Biological Processes and Soft Materials
News continued...
March 18, 2022:
Trent Newman, Bruno Beltran, James McGehee, Daniel Elnatana, Cori Cahoon, Michael Paddy, Daniel Chua,
Andy Spakowitz, and Sean Burgess published "Diffusion and distal linkages govern interchromosomal
dynamics during meiotic prophase" in PNAS.
January 31, 2022:
Sayantan Dutta has joined the Spakowitz lab. Welcome to the group, and we look forward to working with you.
January 25, 2022:
Ashesh Ghosh and Andy Spakowitz published "Statistical behavior of nonequilibrium and living biological systems subjected to active and thermal fluctuations" in Physical Review E.
November 16, 2021:
Luke Balhorn successfully defended his thesis. Congratulations, Dr. Balhorn!
November 16, 2021:
Joe Wakim, Sarah Sandholtz, and Andy Spakowitz published "Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations" in Biophysical Journal.
October 13, 2021:
Giovanna Bucci, Karim Gadelrab, and Andy Spakowitz published "Free Energy and Dynamics of Annihilation of Topological Defects in Nanoconfined DNA" in Macromolecules.
February 19, 2021:
Pam Cai, Brad Krajina, Andy Spakowitz, and Sarah Heilshorn published "Dynamic light scattering microrheology for soft and living materials" in Soft Matter.
February 9, 2021:
Thomas Habte has joined the Spakowitz group. We look forward to working with you, and welcome to the lab.
December 14, 2020:
Michael Beckinghausen passed his qualifying exam. Excellent work, Michael!
November 13, 2020:
Joe Wakim passed his qualifying exam. Congratulations on a job well done!
November 4, 2020:
Ashesh Ghosh has joined the Spakowitz lab. Welcome to the group, and we look forward to working with you.
October 15, 2020:
Sarah Sandholtz, Deepti Kannan, Bruno Beltran, and Andy Spakowitz published "Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks" in Biophysical Journal.
September 2, 2020:
Mike Beckinghausen, Ariana Tse, and Joe Wakim have joined the Spakowitz lab. We are excited to work with you.
August 10, 2020:
Sarah Sandholtz, Quinn MacPherson, and Andy Spakowitz published "Physical Modeling of the Heritability and Maintenance of Epigenetic Modifications” in PNAS.
August 10, 2020:
Pam Cai, Brad Krajina, and Andy Spakowitz published "Brachiation of a polymer chain in the presence of a dynamic network” as a Rapid Communication in Physical Review E.
August 4, 2020:
Giovanna Bucci and Andy Spakowitz published "Systematic Approach toward Accurate and Efficient DNA Sequencing via Nanoconfinement"
in Macro Letters.
April 23, 2020:
Pam Cai has passed her qualifying exam. Congratulations on a job well done!
April 20, 2020:
Quinn MacPherson, Bruno Beltran, and Andy Spakowitz published "Chromatin Compaction Leads to a Preference for Peripheral Heterochromatin” in Biophysical Journal
March 3, 2020:
Sarah Sandholtz successfully defended her thesis. Congratulations, Dr. Sandholtz!
December 18, 2019:
Andy Spakowitz published "Polymer physics across scales: Modeling the multiscale behavior of functional soft materials and biological systems” in Journal of Chemical Physics
November 15, 2019:
Bruno Beltran, Deepti Kannan, Quinn MacPherson, and Andy Spakowitz published "Geometrical heterogeneity dominates thermal fluctuations in facilitating chromatin contacts” in Physical Review Letters
November 13, 2019:
Paul Rudnicki, Quinn MacPherson, Luke Belhorn, Bob Feng, Jian Qin, Alberto Salleo, and Andy Spakowitz published "Impact of liquid-crystalline chain alignment on charge transport in conducting polymers” in Macromolecules
September 30, 2019: Sarah Sandholtz, Bruno Beltran, and Andy Spakowitz published "Physical modeling of the spreading of epigenetic modifications through
transient DNA looping” in Journal of Physics A: Mathematical and Theoretical.
September 2, 2019: Andy Spakowitz published "Transient Anomalous Diffusion in a
Heterogeneous Environment” in Frontiers in Physics.
June 15, 2019: Deepti Kannan received the Kennedy Thesis Prize, which recognizes the single best undergraduate theses in humanities, social sciences, natural sciences, and engineering and applied sciences. Well done, Deepti!
April 17, 2019: Brad Krajina successfully defended his thesis. Congratulations, Dr. Krajina!
November 27, 2018: Quinn MacPherson, Bruno Beltran, and Andy Spakowitz published "Bottom–up modeling of chromatin segregation due to epigenetic modifications” in PNAS.
October 1, 2018: Brad Krajina, Audrey Zhu, Sarah Heilshorn, and Andy Spakowitz published "Active DNA Olympic Hydrogels Driven by Topoisomerase Activity” in Physical Review Letters.
June 18, 2018: Bruno Beltran successfully passed his Biophysics qualifying exam. Great job, Bruno!
May 24, 2018: Shifan Mao, Quinn MacPherson, Chunzi Liu, and Andy Spakowitz published "Thermodynamic Model of Solvent Effects in Semiflexible Diblock and Random Copolymer Assembly” in Macromolecules.
February 9, 2018: Shifan Mao, Quinn MacPherson, and Andy Spakowitz published "Polymer semiflexibility induces nonuniversal phase transitions in diblock copolymers” in Physical Review Letters.
December 19, 2017: Shifan Mao, Quinn MacPherson, and Andy Spakowitz published "Fluctuation Effects in Semiflexible Diblock Copolymers” in Macro Letters.
December 15, 2017: Brad Krajina, Carolina Tropini, Audrey Zhu, Philip DiGiacomo, Justin Sonnenburg, Sarah Heilshorn, and Andy Spakowitz published "Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials” in ACS Central Science.
August 2, 2017: Shifan Mao successfully defended his thesis. Congratulations, Shifan!
March 23, 2017: Shifan Mao, Quinn MacPherson, Jian Qin, and Andy Spakowitz published "Field-theoretic simulations of random copolymers with structural rigidity” in Soft Matter.
March 10, 2017: Kat Pilyugina, Brad Krajina, Andy Spakowitz, and Jay Schieber published "Buckling a Semiflexible Polymer Chain under Compression” in Polymers.
January 31, 2017: Tom Lampo, Stella Stylianidou, Mikael Backlund, Paul Wiggins, and Andy Spakowitz published "Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior” in Biophysical Journal.
January 13, 2017: Lena Koslover, Mario Díaz de la Rosa, and Andy Spakowitz published ”Crowding and hopping in a protein's diffusive transport on DNA” in Journal of Physics A: Mathematical and Theoretical.
November 15, 2016: Sonya Mollinger, Alberto Salleo, and Andy Spakowitz published ”Anomalous Charge Transport in Conjugated Polymers Reveals Underlying Mechanisms of Trapping and Percolation” in ACS Central Science.
October 4, 2016: Brad Krajina and Andy Spakowitz published "Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation" in Biophysical Journal.
July 13, 2016: Tom Lampo successfully defended his thesis. Great job, Tom!
July 13, 2016: Sherrie Zheng has joined the Spakowitz lab as our Administrative Assistant. Welcome, Sherrie.
June 2, 2016: Sarah Sandholtz successfully passed her Chemistry Progress Report. Great job, Sarah!
June 1, 2016: Shifan Mao, Quinn MacPherson, Steve He, Elyse Coletta, and Andy Spakowitz published "Impact of Conformational and Chemical Correlations on Microphase Segregation in Random Copolymers" in Macromolecules.
May 25, 2016: Sonya Mollinger successfully defended her thesis. Congratulations, Sonya!
April 8, 2016: Quinn MacPherson has successfully passed his qualifying exam. Great job, Quinn!
April 1, 2016: Quinn MacPherson has been selected to receive an NSF Graduate Fellowship. Congratulations to Quinn for this well-deserved honor!
January 22, 2016: Tom Lampo, Andrew Kennard, and Andy Spakowitz published “Physical modeling of dynamic coupling of chromosomal loci” in Biophysical Journal.
August 14, 2015: Andy is on sabbatical at the University of Chicago, Institute for Molecular Engineering until March 2016.
August 4, 2015: Pete Mulligan, Yi-Ju Chen, Rob Phillips, and Andy Spakowitz published "Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics" in Biophysical Journal.
June 22, 2015: Sonya Mollinger, Brad Krajina, Rodrigo Noriega, Alberto Salleo, and Andy Spakowitz published “Percolation, tie-molecules, and the microstructural determinants of charge transport in semicrystalline conjugated polymers” in Macro Letters.
June 1, 2015: Quinn MacPherson has joined the Spakowitz Lab. Welcome, Quinn!
May 21, 2015: Brad Krajina has been selected to receive the Bio-X Bowes Graduate Student Fellowship. Congratulations, Brad!
March 31, 2015: Sarah Sandholtz has been selected to receive an NSF Graduate Fellowship. Congratulations to Sarah for this well-deserved honor!
March 20, 2015: Sarah Sandholtz has joined the Spakowitz Lab. Welcome, Sarah!
January 8, 2015: Pete Mulligan, Lena Koslover and Andy Spakowitz published "Thermodynamic model of heterochromatin formation through epigenetic regulation" in Journal of Physics: Condensed Matter.
January 5, 2015: Tom Lampo, Nathan Kuwada, Paul Wiggins and Andy Spakowitz published "Physical Modeling of Chromosome Segregation in Escherichia coli Reveals Impact of Force and DNA Relaxation" in Biophysical Journal.
December 10, 2014: Nick Cordella, Tom Lampo, Nick Melosh and Andy Spakowitz published "Membrane indentation triggers clathrin lattice reorganization and fluidization" in Soft Matter.
December 10, 2014: Yi-Ju Chen, Stephanie Johnson, Pete Mulligan, Andy Spakowitz and Rob Phillips published "Modulation of DNA loop lifetimes by the free energy of loop formation" in PNAS.
September 30, 2014: Nick Cordella’s poster entitled "Membrane Indentation Triggers Clathrin Lattice Reorganization and Fluidization” received the Poster Award at the Korea-U.S. Forum on Nanotechnology. Congratulations, Nick!
September 23, 2014: The Spakowitz Lab has moved to the new location in Clark Center S231. Stop by if you're in the neighborhood.
September 19, 2014: Congratulations to PhD student Brad Krajina for passing his qualifying exam and ascending to PhD candidacy!
July 21, 2014: Jules VanDersarl, Shafigh Mehraeen, Alia Schoen, Sarah Heilshorn, Andy Spakowitz, and Nick Melosh published "Rheology and simulation of 2-dimensional clathrin protein network assembly" in Soft Matter.
July 21, 2014: Lena Koslover and Andy Spakowitz published "Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure" in Physical Review E.
March 31, 2014: Brad Krajina has joined the Spakowitz Lab. Welcome, Brad!
April 1, 2013: Nick Cordella, Tom Lampo, Shafigh Mehraeen, and Andy Spakowitz published "Membrane Fluctuations Destabilize Clathrin Protein Lattice Order" in Biophysical Journal
September 23, 2013: Rodrigo Noriega, Alberto Salleo, and Andy Spakowitz published "Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers" in the Proceedings of the National Academy of Sciences.
September 12, 2013:
Alia P. Schoen, Nicholas Cordella, Shafigh Mehraeen, Manickam Adhimoolam Arunagirinathan, Andrew J. Spakowitz, and Sarah C. Heilshorn published
"Dynamic remodeling of disordered protein aggregates is an alternative pathway to achieve robust self-assembly of nanostructures"
in Soft Matter.
July 26, 2013: Elena Koslover and Andy Spakowitz published "Discretizing elastic chains for coarse-grained polymer models" in Soft Matter
May 23, 2013: Tom Lampo has been selected to receive a Bio-X Stanford Interdisciplinary Graduate Fellowship (SIGF). Congratulations Tom on this well-deserved honor!
April 4, 2013:
Shifan Mao has joined the Spakowitz Lab. Welcome Shifan!
February 15, 2013:
Elena Koslover and Andy Spakowitz published
"Systemic Coarse-Graining of Microscale Polymer Models as Effective Elastic Chains"
in Macromolecules
January 22, 2013: Lena Koslover successfully defended her thesis. Congratulations Lena!
January 14, 2013:
Mario Díaz de la Rosa and Andy Spakowitz, in collaboration with the
McAdams and Shapiro labs at Stanford, published
"Caulobacter chromosome in vivo configuration matches model
predictions for a supercoiled polymer in a cell-like confinement"
in PNAS