selected publications
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book
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conference proceeding
- Action at a distance along the microtubule couples kinesin motors. Biophysical Journal. 440A-440A. 2023
- Coordination without communication in ant excavation. Integrative and Comparative Biology. S16-S17. 2022
- Long-Range Coupling between Kinesins Regulates Collective Motor Behavior. Biophysical Journal. 289A-289A. 2021
- Mechanisms of Bidirectional Transport of Misaligned Chromosomes in Mitosis. Biophysical Journal. 158A-158A. 2019
- A physical model for fission yeast mitosis: from spindle formation through chromosome segregation.. Molecular Biology of the Cell. 2018
- Active matter with intent: clog control in excavating collectives 2018
- Emergent Polar Organization and Bundling of Nematic Filaments Driven by Crosslinking Motors 2018
- Mechanisms of selective transport through nuclear pore complex mimics 2018
- Model of mitotic spindle self-assembly without motor proteins 2018
- Self-organized band state of driven hard needles 2018
- Mechanisms of Selective Transport through the Nuclear Pore Complex. Biophysical Journal. 428A-428A. 2018
- Minimal Ingredients for Coupled Spindle Assembly and Chromosome Bi-orientation in a Computational Model of Fission Yeast Mitosis. Biophysical Journal. 650A-650A. 2018
- Organization and Dynamics of Gliding Flexible Filaments Jeffrey M. Moore. Biophysical Journal. 650A-650A. 2018
- Synthetic Mimics of the Nuclear Pore Complex. Biophysical Journal. 630A-631A. 2018
- Minimal ingredients for coupled spindle assembly and chromosome bi-orientation in a computational model of fission yeast mitosis.. Molecular Biology of the Cell. 2017
- The Effects of Microtubule Length, Dynamics and Bundling on Spindle Assembly.. Molecular Biology of the Cell. 2017
- Regulation of Mitotic Microtubule Dynamic Instability in Monopolar Spindles by Bundling and Kinetochore Attachment. The FASEB Journal. 2017
- Physical determinants of bipolar mitotic spindle assembly and stability. Molecular Biology of the Cell. 2016
- Improving representation in physical sciences using a departmental action team. 264-267. 2016
- Effects of Obstacle Binding and Bound Mobility in a Lattice Model of Protein Diffusion. Biophysical Journal. 596A-596A. 2016
- Effects of Obstacle Binding and Bound Mobility in a Lattice Model of Protein Diffusion. Biophysical Journal. 596A-596A. 2016
- Modeling the Microscopic to Macroscopic Dynamics of Actively Streaming Microtubule Suspensions. Biophysical Journal. 351A-351A. 2014
- Physical Determinants of Bipolar Mitotic Spindle Assembly and Stability in Fission Yeast. Biophysical Journal. 432A-432A. 2014
- Physical Effects Controlling Flock Formation in Systems of Self-Propelled Rods. Biophysical Journal. 508A-508A. 2013
- The Role of Kinesin-8 Proteins in Kinetochore Movements and Spindle Dynamics in Fission Yeast. Biophysical Journal. 327A-327A. 2013
- Accommodating drift in hidden Markov analysis of single-molecule data. ACS National Meeting Book of Abstracts. 2011
- Human TBP Bending of DNA Measured at the Single Molecule Level. Biophysical Journal. 57A-57A. 2009
- PHYS 143-Using quantitative theory to help understand helicase unwinding. ACS National Meeting Book of Abstracts. 2008
- Control of TGF-beta/Smad signaling. Biophysical Journal. 647A-647A. 2007
- Elasticity of short DNA molecules: Quantitative agreement between theory and experiment. Biophysical Journal. 165A-165A. 2007
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journal article
- Bacterial efflux pump modulators prevent bacterial growth in macrophages and under broth conditions that mimic the host environment. mBio. 2023
- Distinct regions of the kinesin-5 C-terminal tail are essential for mitotic spindle midzone localization and sliding force. Proceedings of the National Academy of Sciences of USA. 2023
- Bacterial Efflux Pump Modulators Prevent Bacterial Growth in Macrophages and Under Broth Conditions that Mimic the Host Environment. 2023
- Distinct regions of the kinesin-5 C-terminal tail are essential for mitotic spindle midzone localization and sliding force. 2023
- Quantifying Yeast Microtubules and Spindles Using the Toolkit for Automated Microtubule Tracking (TAMiT). Biomolecules. 2023
- Agitated ants: regulation and self-organization of incipient nest excavation via collisional cues. Journal of the Royal Society Interface. 2023
- The kinesin-5 protein Cut7 moves bidirectionally on fission yeast spindles with activity that increases in anaphase. Journal of Cell Science. 2023
- Quantifying yeast microtubules and spindles using the Toolkit for Automated Microtubule Tracking (TAMiT). 2023
- Motor guidance by long-range communication on the microtubule highway. Proceedings of the National Academy of Sciences of USA. 2022
- Active Condensation of Filaments Under Spatial Confinement. Frontiers in Physics. 2022
- Toward Task Capable Active Matter: Learning to Avoid Clogging in Confined Collectives via Collisions. Frontiers in Physics. 2022
- Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies. eLife. 2022
- A new view of how cytoplasmic viscosity affects microtubule dynamics. Developmental Cell. 419-420. 2022
- Motor guidance by long-range communication through the microtubule highway. Biophysical Journal. 400A-400A. 2022
- Modeling spatiotemporally varying protein-protein interactions in CyLaKS, the Cytoskeleton Lattice-based Kinetic Simulator. The European Physical Journal E: soft Matter and Biological Physics. 2021
- Chiral self-sorting of active semiflexible filaments with intrinsic curvature. Soft Matter. 4559-4565. 2021
- Comparison of explicit and mean-field models of cytoskeletal filaments with crosslinking motors. The European Physical Journal E: soft Matter and Biological Physics. 2021
- Collective motion of driven semiflexible filaments tuned by soft repulsion and stiffness. Soft Matter. 9436-9442. 2020
- Mechanisms of Chromosome biorientation and bipolar spindle assembly analyzed by computational modeling. eLife. 2020
- Bound-State Diffusion due to Binding to Flexible Polymers in a Selective Biofilter. Biophysical Journal. 376-385. 2020
- Design principles of selective transport through biopolymer barriers. Physical Review E. 2019
- Theory of microtubule length regulation in antiparallel overlaps 2019
- Bound-state diffusion due to binding to flexible polymers in a selective biofilter 2019
- Design principles of selective transport through biopolymer barriers 2019
- Mechanisms of chromosome biorientation and bipolar spindle assembly analyzed by computational modeling 2019
- Theory of Cytoskeletal Reorganization during Cross-Linker-Mediated Mitotic Spindle Assembly. Biophysical Journal. 1719-1731. 2019
- Theory of cytoskeletal reorganization during crosslinker-mediated mitotic spindle assembly 2018
- Collective clog control: Optimizing traffic flow in confined biological and robophysical excavation. Science. 672-+. 2018
- Analytical structure, dynamics, and coarse graining of a kinetic model of an active fluid. Physical Review Fluids. 2017
- Effects of soft interactions and bound mobility on diffusion in crowded environments: a model of sticky and slippery obstacles. Physical Biology. 2017
- Kinesin-5-independent mitotic spindle assembly requires the antiparallel microtubule crosslinker Ase1 in fission yeast. Nature Communications. 2017
- Contributions of Microtubule Dynamic Instability and Rotational Diffusion to Kinetochore Capture. Biophysical Journal. 552-563. 2017
- Physical determinants of bipolar mitotic spindle assembly and stability in fission yeast. Science Advances. 2017
- Kinesin-8 effects on mitotic microtubule dynamics contribute to spindle function in fission yeast. Molecular Biology of the Cell. 3490-3514. 2016
- Phase-plane analysis of the totally asymmetric simple exclusion process with binding kinetics and switching between antiparallel lanes. Physical Review E. 2016
- Motor Protein Accumulation on Antiparallel Microtubule Overlaps. Biophysical Journal. 2034-2043. 2016
- Microscopic origins of anisotropic active stress in motor-driven nematic liquid crystals. Soft Matter. 2676-2687. 2016
- Hysteresis, reentrance, and glassy dynamics in systems of self-propelled rods. Physical Review E. 2015
- Multiscale modeling and simulation of microtubule-motor-protein assemblies. Physical Review E. 2015
- Multiscale Polar Theory of Microtubule and Motor-Protein Assemblies. Physical Review Letters. 2015
- Regulation of Chromosome Speeds in Mitosis. Cellular and Molecular Bioengineering. 418-430. 2013
- Biophysics of filament length regulation by molecular motors. Physical Biology. 2013
- Linear aggregation and liquid-crystalline order: comparison of Monte Carlo simulation and analytic theory. Journal of Materials Chemistry. 10366-10383. 2010
- Microtubule Depolymerization by the Kinesin-8 Motor Kip3p: A Mathematical Model. Biophysical Journal. 3050-3064. 2009
- Activating and inhibiting connections in biological network dynamics. Biology Direct. 2008
- Two-state model for helicase translocation and unwinding of nucleic acids. Physical Review E. 2008
- Multiple pattern matching: a Markov chain approach. Journal of Mathematical Biology. 51-92. 2008
- Elasticity of short DNA molecules:: Theory and experiment for contour lengths of 0.6-7 μm. Biophysical Journal. 4360-4373. 2007
- TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. Journal of Molecular Biology. 619-632. 2007
- PHYS 702-Elasticity of short DNA molecules: A combined experimental and theoretical study. ACS National Meeting Book of Abstracts. 2007
- Entropic elasticity of DNA with a permanent kink. Macromolecules. 8816-8821. 2006
- Systems theory of Smad signalling. IET Systems Biology. 412-424. 2006
- Using the nucleotide substitution rate matrix to detect horizontal gene transfer. BMC Bioinformatics. 2006
- Incorporating expression data in metabolic modeling: A case study of lactate dehydrogenase. Journal of Theoretical Biology. 464-474. 2006
- Controlled irradiative formation of penitentes. Physical Review Letters. 2006
- Velocity and processivity of helicase unwinding of double-stranded nucleic acids. Journal of Physics: Condensed Matter. S3851-S3869. 2005
- Erratum: Opening of nucleic-acid double strands by helicases: Active versus passive opening [Phys. Rev. E 71, 011904 (2005)]. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 2005
- Opening of nucleic-acid double strands by helicases:: Active versus passive opening -: art. no. 011904. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 2005
- A motor that makes its own track: Helicase unwinding of DNA. Physical Review Letters. 2003
- Helicase opening of duplex nucleic acids: active versus passive opening. Biophysical Journal. 13A-13A. 2003
- Collapsing bacterial cylinders. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 2001
- Theory of structure formation in snowfields motivated by penitentes, suncups, and dirt cones. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 2001
- Electrostatic Edge Instability of Lipid Membranes. Physical Review Letters. 1598-1601. 1999