Now showing items 1-20 of 586

    • A Choose-Your-Own-Adventure-Style Virtual Lab Activity 

      Warning, Lauren A.; Kobylianskii, Krista (2021)
      Especially in the wake of the recent COVID-19 pandemic, which has caused universities across the globe to suspend in-person classes, online alternatives for laboratory activities are needed. Here, we report a choose-your-own-adventure (CYOA)-style activity, in which undergraduate general chemistry students influence the observed outcome of a prerecorded ...
    • A collagen glucosyltransferase drives lung adenocarcinoma progression in mice 

      Guo, Hou-Fu; Bota-Rabassedas, Neus; Terajima, Masahiko; Leticia Rodriguez, B.; Gibbons, Don L.; (2021)
      Cancer cells are a major source of enzymes that modify collagen to create a stiff, fibrotic tumor stroma. High collagen lysyl hydroxylase 2 (LH2) expression promotes metastasis and is correlated with shorter survival in lung adenocarcinoma (LUAD) and other tumor types. LH2 hydroxylates lysine (Lys) residues on fibrillar collagen’s amino- and ...
    • A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures 

      Boninsegna, Lorenzo; Banisch, Ralf; Clementi, Cecilia; Center for Theoretical Biological Physics (2018)
      Macromolecular systems are composed of a very large number of atomic degrees of freedom. There is strong evidence suggesting that structural changes occurring in large biomolecular systems at long time scale dynamics may be captured by models coarser than atomistic, although a suitable or optimal coarse-graining is a priori unknown. Here we propose ...
    • A deterministic model for one-dimensional excluded flow with local interactions 

      Zarai, Yoram; Margaliot, Michael; Kolomeisky, Anatoly B. (2017)
      Natural phenomena frequently involve a very large number of interacting molecules moving in confined regions of space. Cellular transport by motor proteins is an example of such collective behavior. We derive a deterministic compartmental model for the unidirectional flow of particles along a one-dimensional lattice of sites with nearest-neighbor ...
    • A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling 

      Bocci, Federico; Jolly, Mohit Kumar; George, Jason Thomas; Levine, Herbert; Onuchic, José Nelson; (2018)
      Epithelial-mesenchymal transition (EMT) and cancer stem cell (CSCs) formation are two fundamental and well-studied processes contributing to cancer metastasis and tumor relapse. Cells can undergo a partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype or a complete EMT to attain a mesenchymal one. Similarly, cells can reversibly gain ...
    • A New High-Performance Gadonanotube-Polymer Hybrid Material for Stem Cell Labeling and Tracking by MRI 

      Moghaddam, Sakineh E.; Hernández-Rivera, Mayra; Zaibaq, Nicholas G.; Ajala, Afis; Cabreira-Hansen, Maria da Graça; (2018)
      A gentle, rapid method has been developed to introduce a polyacrylic acid (PAA) polymer coating on the surface of gadonanotubes (GNTs) which significantly increases their dispersibility in water without the need of a surfactant. As a result, the polymer, with its many carboxylic acid groups, coats the surface of the GNTs to form a new GNT-polymer ...
    • A room-temperature mid-infrared photodetector for on-chip molecular vibrational spectroscopy 

      Zheng, Bob; Zhao, Hangqi; Cerjan, Ben; Yazdi, Sadegh; Ringe, Emilie; (2018)
      Infrared (IR) photodetection is of major scientific and technical interest since virtually all molecules exhibit characteristic vibrational modes in the mid-infrared region of the spectrum, giving rise to molecular spectroscopy and chemical imaging in this wavelength range. High-resolution IR spectroscopies, such as Fourier Transform IR spectroscopy, ...
    • A symmetrical method to obtain shear moduli from microrheology 

      Nishi, Kengo; Kilfoil, Maria L.; Schmidt, Christoph F.; MacKintosh, F.C. (2018)
      Passive microrheology typically deduces shear elastic loss and storage moduli from displacement time series or mean-squared displacements (MSD) of thermally fluctuating probe particles in equilibrium materials. Common data analysis methods use either Kramers–Kronig (KK) transformation or functional fitting to calculate frequency-dependent loss and ...
    • A synthetic circuit for buffering gene dosage variation between individual mammalian cells 

      Yang, Jin; Lee, Jihwan; Land, Michelle A.; Lai, Shujuan; Igoshin, Oleg A.; (2021)
      Precise control of gene expression is critical for biological research and biotechnology. However, transient plasmid transfections in mammalian cells produce a wide distribution of copy numbers per cell, and consequently, high expression heterogeneity. Here, we report plasmid-based synthetic circuits – Equalizers – that buffer copy-number variation ...
    • A TiO2/FeMnP Core/Shell Nanorod Array Photoanode for Efficient Photoelectrochemical Oxygen Evolution 

      Schipper, Desmond E.; Zhao, Zhenhuan; Leitner, Andrew P.; Xie, Lixin; Qin, Fan; (2017)
      A variety of catalysts have recently been developed for electrocatalytic oxygen evolution, but very few of them can be readily integrated with semiconducting light absorbers for photoelectrochemical or photocatalytic water splitting. Here, we demonstrate an efficient core/shell photoanode with a highly active oxygen evolution electrocatalyst shell ...
    • A zero-dimensional view of atmospheric degradation of levoglucosan (LEVCHEM_v1) using numerical chamber simulations 

      Suciu, Loredana G.; Griffin, Robert J.; Masiello, Caroline A. (2021)
      Here, we developed a zero-dimensional (0-D) modeling framework (LEVCHEM_v1) to provide insights into the atmospheric degradation of a key tracer emitted during biomass burning – levoglucosan (LEV), while additionally exploring its effects on the dynamics of secondary organic aerosols (SOA) and other gases. For this, we updated existing chemical ...
    • Absorption Spectroscopy of an Individual Fano Cluster 

      Yorulmaz, Mustafa; Hoggard, Anneli; Zhao, Hangqi; Wen, Fangfang; Chang, Wei-Shun; (2016)
      Plasmonic clusters can exhibit Fano resonances with unique and tunable asymmetric line shapes, which arise due to the coupling of bright and dark plasmon modes within each multiparticle structure. These structures are capable of generating remarkably large local electromagnetic field enhancements and should give rise to high hot carrier yields relative ...
    • Accuracy of Substrate Selection by Enzymes Is Controlled by Kinetic Discrimination 

      Banerjee, Kinshuk; Kolomeisky, Anatoly B.; Igoshin, Oleg A.; Center for Theoretical Biological Physics (2017)
      Enzymes have the remarkable ability to select the correct substrate from the pool of chemically similar molecules. The accuracy of such a selection is determined by differences in the free-energy profiles for the right and wrong reaction pathways. Here, we investigate which features of the free-energy landscape govern the variation and minimization ...
    • Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals 

      Garza, Alejandro J.; Alencar, Ana G. Sousa; Scuseria, Gustavo E. (2016)
      Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the ...
    • Active patterning and asymmetric transport in a model actomyosin network 

      Wang, Shenshen; Wolynes, Peter G.; Center for Theoretical Biological Physics (2013)
      Cytoskeletal networks, which are essentially motor-filament assemblies, play a major role in many developmental processes involving structural remodeling and shape changes. These are achieved by nonequilibrium self-organization processes that generate functional patterns and drive intracellular transport. We construct a minimal physical model that ...
    • Adsorption and Unfolding of a Single Protein Triggers Nanoparticle Aggregation 

      (2016)
      The response of living systems to nanoparticles is thought to depend on the protein corona, which forms shortly after exposure to physiological fluids and which is linked to a wide array of pathophysiologies. A mechanistic understanding of the dynamic interaction between proteins and nanoparticles and thus the biological fate of nanoparticles and ...
    • Adsorption of a Protein Monolayer via Hydrophobic Interactions Prevents Nanoparticle Aggregation under Harsh Environmental Conditions 

      (2013)
      We find that citrate-stabilized gold nanoparticles aggregate and precipitate in saline solutions below the NaCl concentration of many bodily fluids and blood plasma. Our experiments indicate that this is due to complexation of the citrate anions with Na+ cations in solution. A dramatically enhanced colloidal stability is achieved when bovine serum ...
    • Adverse Effect of PTFE Stir Bars on the Covalent Functionalization of Carbon and Boron Nitride Nanotubes Using Billups–Birch Reduction Conditions 

      de los Reyes, Carlos A.; Smith McWilliams, Ashleigh D.; Hernández, Katharyn; Walz-Mitra, Kendahl L.; Ergülen, Selin; (2019)
      The functionalization of nanomaterials has long been studied as a way to manipulate and tailor their properties to a desired application. Of the various methods available, the Billups–Birch reduction has become an important and widely used reaction for the functionalization of carbon nanotubes (CNTs) and, more recently, boron nitride nanotubes. ...
    • Aged black carbon in marine sediments and sinking particles 

      Coppola, Alysha I.; Ziolkowski, Lori A.; Masiello, Caroline A.; Druffel, Ellen R.M. (2014)
      We report measurements of oceanic black carbon (BC) to determine the sources of BC to abyssal marine sediments in the northeast Pacific Ocean. We find that the average 14C age of BC is older (by 6200 ± 2200 14C years) than that of the concurrently deposited non-BC sedimentary organic carbon. We investigate sources of aged BC to sediments by measuring ...
    • Aging, Jamming, and the Limits of Stability of Amorphous Solids 

      Lubchenko, Vassiliy; Wolynes, Peter G.; Center for Theoretical Biological Physics (2018)
      Apart from not having crystallized, supercooled liquids can be considered as being properly equilibrated and thus can be described by a few thermodynamic control variables. In contrast, glasses and other amorphous solids can be arbitrarily far away from equilibrium and require a description of the history of the conditions under which they formed. ...