Now showing items 1-20 of 31

    • AC Electric Fields Drive Steady Flows in Flames 

      Drews, Aaron M.; Cademartiri, Ludovico; Chemama, Michael Leopold; Brenner, Michael P.; Whitesides, George M.; Bishop, Kyle J. M. (American Physical Society (APS), 2012)
      We show that time-oscillating electric fields applied to plasmas present in flames create steady flows of gas. Ions generated within the flame move in the field and migrate a distance δ before recombining; the net flow of ...
    • Action Potential Initiation in the Hodgkin-Huxley Model 

      Colwell, Lucy J.; Brenner, Michael (Public Library of Science, 2009)
      A recent paper of B. Naundorf et al. described an intriguing negative correlation between variability of the onset potential at which an action potential occurs (the onset span) and the rapidity of action potential initiation ...
    • An adaptive reduction algorithm for efficient chemical calculations in global atmospheric chemistry models 

      Santillana, Mauricio; Le Sager, Philippe; Jacob, Daniel James; Brenner, Michael P. (Elsevier BV, 2010)
      We present a computationally efficient adaptive method for calculating the time evolution of the concentrations of chemical species in global 3-D models of atmospheric chemistry. Our strategy consists of partitioning the ...
    • Cavitation in Linear Bubbles 

      Brenner, Michael P. (Cambridge University Press, 2009)
      Recent work has developed a beautiful model system for studying the energy focusing and heating power of collapsing bubbles. The bubble is effectively one-dimensional and the collapse and heating can be quantitatively ...
    • Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex 

      Colwell, Lucy Jane; Brenner, Michael P.; Ribbeck, Katharina; Gilson, Michael (Public Library of Science, 2010)
      Nuclear pore complexes (NPCs) are highly selective filters that control the exchange of material between nucleus and cytoplasm. The principles that govern selective filtering by NPCs are not fully understood. Previous ...
    • Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs 

      Mallarino, Ricardo; Campas, O.; Fritz, Joerg; Burns, K. J.; Weeks, Olivia Grace; Brenner, Michael P.; Abzhanov, Arkhat (Proceedings of the National Academy of Sciences, 2012)
      The astonishing variation in the shape and size of bird beaks reflects a wide range of dietary specializations that played an important role in avian diversification. Among Darwin's finches, ground finches (Geospiza spp.) ...
    • Computations and Algorithms in Physical and Biological Problems 

      Qin, Yu (2014-06-06)
      This dissertation presents the applications of state-of-the-art computation techniques and data analysis algorithms in three physical and biological problems: assembling DNA pieces, optimizing self-assembly yield, and ...
    • Conservation Weighting Functions Enable Covariance Analyses to Detect Functionally Important Amino Acids 

      Colwell, Lucy J.; Brenner, Michael P.; Murray, Andrew W. (Public Library of Science, 2014)
      The explosive growth in the number of protein sequences gives rise to the possibility of using the natural variation in sequences of homologous proteins to find residues that control different protein phenotypes. Because ...
    • Deriving Finite Sphere Packings 

      Arkus, Natalie; Manoharan, Vinothan N.; Brenner, Michael P. (Society for Industrial and Applied Mathematics, 2011)
      Sphere packing problems have a rich history in both mathematics and physics; yet, relatively few analytical analyses of sphere packings exist, and answers to seemingly simple questions are unknown. Here, we present an ...
    • Dynamic Equilibrium Mechanism for Surface Nanobubble Stabilization 

      Brenner, Michael; Lohse, Detlef (American Physical Society, 2008)
      Recent experiments have convincingly demonstrated the existence of surface nanobubbles on submerged hydrophobic surfaces. However, classical theory dictates that small gaseous bubbles quickly dissolve because their large ...
    • Excitability Constraints on Voltage-Gated Sodium Channels 

      Angelino, Elaine; Brenner, Michael (Public Library of Science, 2007)
      We study how functional constraints bound and shape evolution through an analysis of mammalian voltage-gated sodium channels. The primary function of sodium channels is to allow the propagation of action potentials. Since ...
    • Explosively launched spores of ascomycete fungi have drag-minimizing shapes 

      Roper, M.; Pepper, R. E.; Brenner, Michael P.; Pringle, Anne E. (Proceedings of the National Academy of Sciences, 2008)
      The forcibly launched spores of ascomycete fungi must eject through several millimeters of nearly still air surrounding fruiting bodies to reach dispersive air flows. Because of their microscopic size, spores experience ...
    • The Free-Energy Landscape of Clusters of Attractive Hard Spheres 

      Meng, Guangnan; Arkus, Natalie; Brenner, Michael P.; Manoharan, Vinothan N. (American Association for the Advancement of Science, 2010)
      The study of clusters has provided the most tangible link between local geometry and bulk condensed matter. But experiments have not yet systematically explored the thermodynamics of even the smallest clusters. Here we ...
    • A geometrical approach to computing free-energy landscapes from short-ranged potentials 

      Holmes-Cerfon, M.; Gortler, Steven J.; Brenner, Michael P. (Proceedings of the National Academy of Sciences, 2012)
      Particles interacting with short-ranged potentials have attracted increasing interest, partly for their ability to model mesoscale systems such as colloids interacting via DNA or depletion. We consider the free-energy ...
    • Linear Dynamics of Ion Sputtered Surfaces: Instability, Stability and Bifurcations 

      Davidovitch, Benny; Aziz, Michael; Brenner, Michael (Insitute of Physics Publishing, 2009)
      The linear dynamics of ion sputtered solids is essential to understanding the evolution of ordered and disordered surface patterns. We review the existing models of linear dynamics and point out qualitative discrepancies ...
    • Mechanism of nanostructure movement under an electron beam and its application in patterning 

      Seminara, Agnese; Pokroy, Boaz; Kang, Sung H.; Brenner, Michael P.; Aizenberg, Joanna (American Physical Society (APS), 2011)
      In electron microscopy, the motion of the sample features due to the interaction with the electron beam has been traditionally regarded as a detrimental effect. Uncontrolled feature displacement produces artifacts both in ...
    • Minimal Energy Clusters of Hard Spheres with Short Range Attractions 

      Arkus, Natalie; Manoharan, Vinothan N.; Brenner, Michael P. (American Physical Society, 2009)
      We calculate the ground states of hard-sphere clusters, in which n identical hard spherical particles bind by isotropic short-ranged attraction. Combining graph theoretic enumeration with basic geometry, we analytically ...
    • Multiple Bifurcation Types and the Linear Dynamics of Ion Sputtered Surfaces 

      Madi, Charbel S.; Davidovitch, Benny; George, H. Bola; Norris, Scott A.; Brenner, Michael; Aziz, Michael (American Physical Society, 2008)
      We study the patterns formed on ion sputtered Si surfaces as a function of ion energy and incidence angle, and identify a region in parameter space where the flat surface is stable. The boundaries between the stable and ...
    • On the Stabilization of Ion Sputtered Surfaces 

      Davidovitch, Benny; Aziz, Michael; Brenner, Michael (The American Physical Society, 2007)
      The classical theory of ion beam sputtering predicts the instability of a flat surface to uniform ion irradiation at any incidence angle. We relax the assumption of the classical theory that the average surface erosion ...
    • Organization and diffusion in biological and material fabrication problems 

      Mangan, Niall Mari (2013-10-14)
      This thesis is composed of two problems. The first is a systems level analysis of the carbon concentrating mechanism in cyanobacteria. The second presents a theoretical analysis of femtosecond laser melting for the purpose ...