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  • May
    1

    ME 512 Seminar - Aniket Bhattacharya - DNA conformations and dynamics squeezed inside a nano-channel with a sliding gasket

    McCormick - Mechanical Engineering

    3:00 PM L211 Technological Institute

    EVENT DETAILS

    DNA conformations and dynamics squeezed inside a nano-channel with a sliding gasket

    Monday, May 1, 2017
    3:00pm – 4:30pm

    ABSTRACT

    DNA is one of the most important biomolecules in living organism, forms a helix from two intertwined strands with complementary base pairs. Biological functions of a DNA depend on its mechanical properties, which in turn depend on its sequence specificity. Under physiological condition a double stranded DNA (dsDNA) is described as a semi-flexible biopolymer with persistence length of 50 nm,
    while a single-stranded DNA (ssDNA) is quite flexible. Recently straightening a dsDNA inside a nanochannel is being explored as an alternate method to determine DNA sequences at a single molecule level without replication [1,2].

    First, I will present coarse grained (CG) models for fast computations of DNA conformations and dynamics. I will use scaling arguments validated by Brownian dynamics (BD) simulation results performed on the CG models to demonstrate how the equilibrium DNA conformations change inside a nanochannel as one varies the persistence length (stiffness) and the channel width [3,4]. I will then show the transients and the steady states of an initially straightened DNA inside a nanochannel squeezed by a nano-dozer assay [5].

    Finally, I will compare the time dependent density profiles from the BD simulation with those obtained from a Nonlinear Partial Differential Equation (NPDE) approach [5] recently introduced by Khorshid et al. [1,2], and demonstrate how this combined approach can be effectively used to study nonequilibrium dynamics of very long dsDNA segments inside a nanochannel [3].

    ∗Work done in collaboration with Aiqun Huang, Walter Reisner, H.-P. Hsu and Kurt Binder

    1. A. Khorshid, P. Zimmy, D. Tetreault-La Roche, G. Massarelli, T. Sakaue, and W. Reisner, Dynamic Compression of Single Nanochannel Confined DNA via
    a Nanodozer Assay, Phys. Rev. Lett, 113, 268104 (2014).
    2. A. Khorshid, S. Amin, Z. Zhang, T. Sakaue, and W. Reisner, Nonequilibrim Dynamics of Nanochannel Confined DNA, Macromolecules 49, 1933 (2016).
    3. Aiqun Huang, H.-P Hsu, Aniket Bhattacharya, and Kurt Binder, Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete
    versus continuous bond angles, J. Chem. Phys. 143, 243102 (2015).
    4. Aiqun Huang and Aniket Bhattacharya, DNA confined in a two-dimensional strip geometry, Euro Phys. Lett. 106, 18004 (2014).
    5. A. Huang, W. Reisner, and A. Bhattacharya, Dynamics of DNA Squeezed inside a Nanochannel via a Sliding Gasket, Polymers 8, 352 (2016).

    BIOGRAPHY

    BS (Hons) Physics from Presidency College, Kolkata, India l MS (Physics) from University College of Science, Kolkata, India l PhD in Condensed Matter Physics, University of Maryland, College Park l Research Associate at Penn State University l Research Asst. Professor at Michigan State University l UCF Physics - since 2000
    Research Interest: Theoretical and Computational Soft Matter and Biological Physics

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    TIME Monday, May 1, 2017 at 3:00 PM - 4:30 PM

    LOCATION L211 Technological Institute    map it

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    CONTACT Tami Santos    tami.santos@northwestern.edu EMAIL

    CALENDAR McCormick - Mechanical Engineering

  • Apr
    30

    ME Alumni Seminar Series- Apostolos Karafillis

    McCormick - Mechanical Engineering (ME)

    2:00 PM 1.350, Ford Motor Company Engineering Design Center

    EVENT DETAILS

    TIME Tuesday, April 30, 2024 at 2:00 PM - 3:00 PM

    LOCATION 1.350, Ford Motor Company Engineering Design Center    map it

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    CONTACT Jeremy Wells    jeremywells@northwestern.edu EMAIL

    CALENDAR McCormick - Mechanical Engineering (ME)

  • May
    3

    Russ Tedrake, MIT and Toyota Research Institute, "Dexterous Manipulation with Diffusion Policies"

    Center for Robotics and Biosystems (CRB)

    11:30 AM M416, Technological Institute

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    TIME Friday, May 3, 2024 at 11:30 AM - 12:30 PM

    LOCATION M416, Technological Institute    map it

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    CONTACT Amy Nedoss    amy.nedoss@northwestern.edu EMAIL

    CALENDAR Center for Robotics and Biosystems (CRB)

  • May
    8

    Extending Care: A Conversation about Conservation and Futurity

    Block Museum of Art

    6:00 PM Block Museum of Art, Mary and Leigh

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    TIME Wednesday, May 8, 2024 at 6:00 PM - 7:30 PM

    LOCATION Block Museum of Art, Mary and Leigh    map it

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    CONTACT Block Museum of Art    block-museum@northwestern.edu EMAIL

    CALENDAR Block Museum of Art

  • Jun
    10

    Northwestern Engineering PhD Hooding and Master's Degree Recognition Ceremony

    McCormick School of Engineering and Applied Science

    9:00 AM Welsh-Ryan Arena

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    TIME Monday, June 10, 2024 at 9:00 AM - 11:00 AM

    LOCATION Welsh-Ryan Arena   

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    CONTACT Amy Pokrass    amy.pokrass@northwestern.edu EMAIL

    CALENDAR McCormick School of Engineering and Applied Science

  • Jun
    10

    Northwestern Engineering Undergraduate Convocation

    McCormick School of Engineering and Applied Science

    2:00 PM Welsh-Ryan Arena

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    TIME Monday, June 10, 2024 at 2:00 PM - 4:00 PM

    LOCATION Welsh-Ryan Arena   

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    CONTACT Amy Pokrass    amy.pokrass@northwestern.edu EMAIL

    CALENDAR McCormick School of Engineering and Applied Science

  • Aug
    14

    Undergraduate Quantum Summer School

    McCormick School of Engineering and Applied Science

    All Day Ford Motor Company Engineering Design Center

    EVENT DETAILSmore info

    TIME Wednesday, August 14, 2024

    LOCATION Ford Motor Company Engineering Design Center    map it

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    CONTACT Dongyang Li    lidongyang@northwestern.edu EMAIL

    CALENDAR McCormick School of Engineering and Applied Science

  • Aug
    15

    Undergraduate Quantum Summer School

    McCormick School of Engineering and Applied Science

    All Day Ford Motor Company Engineering Design Center

    EVENT DETAILSmore info

    TIME Thursday, August 15, 2024

    LOCATION Ford Motor Company Engineering Design Center    map it

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    CONTACT Dongyang Li    lidongyang@northwestern.edu EMAIL

    CALENDAR McCormick School of Engineering and Applied Science