Now showing items 1-20 of 654

    • 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 general theoretical framework to design base editors with reduced bystander effects 

      Wang, Qian; Yang, Jie; Zhong, Zhicheng; Vanegas, Jeffrey A.; Gao, Xue; (2021)
      Base editors (BEs) hold great potential for medical applications of gene therapy. However, high precision base editing requires BEs that can discriminate between the target base and multiple bystander bases within a narrow active window (4 – 10 nucleotides). Here, to assist in the design of these optimized editors, we propose a discrete-state stochastic ...
    • A litmus test for classifying recognition mechanisms of transiently binding proteins 

      Chakrabarti, Kalyan S.; Olsson, Simon; Pratihar, Supriya; Giller, Karin; Overkamp, Kerstin; (2022)
      Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein ...
    • 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 photochemical C=C cleavage process: toward access to backbone N-formyl peptides 

      Wang, Haopei; Ball, Zachary T. (2021)
      Photo-responsive modifications and photo-uncaging concepts are useful for spatiotemporal control of peptides structure and function. While side chain photo-responsive modifications are relatively common, access to photo-responsive modifications of backbone N–H bonds is quite limited. This letter describes a new photocleavage pathway, affording N-formyl ...
    • 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 VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics 

      Karmi, Ola; Marjault, Henri-Baptiste; Bai, Fang; Roy, Susmita; Sohn, Yang-Sung; (2022)
      Mitochondrial inner NEET (MiNT) and the outer mitochondrial membrane (OMM) mitoNEET (mNT) proteins belong to the NEET protein family. This family plays a key role in mitochondrial labile iron and reactive oxygen species (ROS) homeostasis. NEET proteins contain labile [2Fe-2S] clusters which can be transferred to apo-acceptor proteins. In eukaryotes, ...
    • A wireless millimetric magnetoelectric implant for the endovascular stimulation of peripheral nerves 

      Chen, Joshua C.; Kan, Peter; Yu, Zhanghao; Alrashdan, Fatima; Garcia, Roberto; (2022)
      Implantable bioelectronic devices for the simulation of peripheral nerves could be used to treat disorders that are resistant to traditional pharmacological therapies. However, for many nerve targets, this requires invasive surgeries and the implantation of bulky devices (about a few centimetres in at least one dimension). Here we report the design ...
    • 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 ...