Now showing items 1-20 of 586

    • Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications 

      Iwahara, Junji; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics (2021)
      To perform their functions, transcription factors and DNA-repair/modifying enzymes randomly search DNA in order to locate their specific targets on DNA. Discrete-state stochastic kinetic models have been developed to explain how the efficiency of the search process is influenced by the molecular properties of proteins and DNA as well as by other ...
    • Mechanical Reshaping of Inorganic Nanostructures with Weak Nanoscale Forces 

      Rehn, Sarah M.; Gerrard-Anderson, Theodor M.; Qiao, Liang; Zhu, Qing; Wehmeyer, Geoff; (2021)
      Inorganic nanomaterials are often depicted as rigid structures whose shape is permanent. However, forces that are ordinarily considered weak can exert sufficient stress at the nanoscale to drive mechanical deformation. Here, we leverage van der Waals (VdW) interactions to mechanically reshape inorganic nanostructures from planar to curvilinear. ...
    • Groundwater Remediation of Volatile Organic Compounds Using Nanofiltration and Reverse Osmosis Membranes—A Field Study 

      Ainscough, Thomas J.; Oatley-Radcliffe, Darren L.; Barron, Andrew R. (2021)
      Groundwater contamination by chlorinated hydrocarbons represents a particularly difficult separation to achieve and very little is published on the subject. In this paper, we explore the potential for the removal of chlorinated volatile and non-volatile organics from a site in Bedfordshire UK. The compounds of interest include trichloroethylene (TCE), ...
    • Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system 

      Rao, Satyajit D.; Igoshin, Oleg A.; Center for Theoretical Biological Physics (2021)
      Bacteria use two-component systems (TCSs) to sense environmental conditions and change gene expression in response to those conditions. To amplify cellular responses, many bacterial TCSs are under positive feedback control, i.e. increase their expression when activated. Escherichia coli Mg2+ -sensing TCS, PhoPQ, in addition to the positive feedback, ...
    • Spectral Properties of Effective Dynamics from Conditional Expectations 

      Nüske, Feliks; Koltai, Péter; Boninsegna, Lorenzo; Clementi, Cecilia; Center for Theoretical Biological Physics (2021)
      The reduction of high-dimensional systems to effective models on a smaller set of variables is an essential task in many areas of science. For stochastic dynamics governed by diffusion processes, a general procedure to find effective equations is the conditioning approach. In this paper, we are interested in the spectrum of the generator of the ...
    • Nanoscale Probing of Image-Potential States and Electron Transfer Doping in Borophene Polymorphs 

      Liu, Xiaolong; Wang, Luqing; Yakobson, Boris I.; Hersam, Mark C. (2021)
      Because synthetic 2D materials are generally stabilized by interfacial coupling to growth substrates, direct probing of interfacial phenomena is critical for understanding their nanoscale structure and properties. Using field-emission resonance spectroscopy with an ultrahigh vacuum scanning tunneling microscope, we reveal Stark-shifted image-potential ...
    • Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences 

      Del Valle, Ilenne; Fulk, Emily M.; Kalvapalle, Prashant; Silberg, Jonathan J.; Masiello, Caroline A.; (2021)
      The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open ...
    • 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 ...
    • Mild olefin formation via bio-inspired vitamin B12 photocatalysis 

      Bam, Radha; Pollatos, Alexandros S.; Moser, Austin J.; West, Julian G. (2021)
      Dehydrohalogenation, or elimination of hydrogen-halide equivalents, remains one of the simplest methods for the installation of the biologically-important olefin functionality. However, this transformation often requires harsh, strongly-basic conditions, rare noble metals, or both, limiting its applicability in the synthesis of complex molecules. ...
    • DNA Looping and DNA Conformational Fluctuations Can Accelerate Protein Target Search 

      Felipe, Cayke; Shin, Jaeoh; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics (2021)
      Protein searching and binding to specific sites on DNA is a fundamentally important process that marks the beginning of all major cellular transformations. While the dynamics of protein–DNA interactions in in vitro settings is well investigated, the situation is much more complex for in vivo conditions because the DNA molecules in live cells are ...
    • Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils 

      Yang, David S.; Saeedi, Arash; Davtyan, Aram; Fathi, Mohsen; Sherman, Michael B.; (2021)
      The protein p53 is a crucial tumor suppressor, often called “the guardian of the genome”; however, mutations transform p53 into a powerful cancer promoter. The oncogenic capacity of mutant p53 has been ascribed to enhanced propensity to fibrillize and recruit other cancer fighting proteins in the fibrils, yet the pathways of fibril nucleation and ...
    • Heavy oil viscosity reduction at mild temperatures using palladium acetylacetonate 

      Xu, Yan; Heck, Kimberly N.; Ayala-Orozco, Ciceron; Arredondo, Jacob H.; Zenor, William; (2021)
      Metal-ligand compounds (“MLCs”) have been shown to reduce heavy oil viscosity and upgrade oil quality. However, MLCs generally require high treatment temperatures (around 250 °C), which is undesirably energy-intensive. We identified palladium(II) acetylacetonate (“PdA”) as a model MLC that can operate at mild temperatures (<200 °C). We studied its ...
    • OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations 

      Lu, Wei; Bueno, Carlos; Schafer, Nicholas P.; Moller, Joshua; Jin, Shikai; (2021)
      We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield ...
    • Theoretical Analysis Reveals the Cost and Benefit of Proofreading in Coronavirus Genome Replication 

      Mallory, Joel D.; Mallory, Xian F.; Kolomeisky, Anatoly B.; Igoshin, Oleg A.; Center for Theoretical Biological Physics (2021)
      Severe acute respiratory syndrome coronaviruses have unusually large RNA genomes replicated by a multiprotein complex containing an RNA-dependent RNA polymerase (RdRp). Exonuclease activity enables the RdRp complex to remove wrongly incorporated bases via proofreading, a process not utilized by other RNA viruses. However, it is unclear why the RdRp ...
    • 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 ...
    • Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2 

      Azouz, Nurit P.; Klingler, Andrea M.; Callahan, Victoria; Akhrymuk, Ivan V.; Elez, Katarina; (2021)
      Background: Host proteases have been suggested to be crucial for dissemination of MERS, SARS-CoV, and SARS-CoV-2 coronaviruses, but the relative contribution of membrane versus intracellular proteases remains controversial. Transmembrane serine protease 2 (TMPRSS2) is regarded as one of the main proteases implicated in the coronavirus S protein ...
    • Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity 

      Hoffmann, Markus; Hofmann-Winkler, Heike; Smith, Joan C.; Krüger, Nadine; Arora, Prerna; (2021)
      Background: Antivirals are needed to combat the COVID-19 pandemic, which is caused by SARS-CoV-2. The clinically-proven protease inhibitor Camostat mesylate inhibits SARS-CoV-2 infection by blocking the virus-activating host cell protease TMPRSS2. However, antiviral activity of Camostat mesylate metabolites and potential viral resistance have not ...
    • Chemical Interface Damping of Surface Plasmon Resonances 

      Lee, Stephen A.; Link, Stephan; Smalley Curl Institute (2021)
      ConspectusMetal nanoparticles have been utilized for a vast amount of plasmon enhanced spectroscopies and energy conversion devices. Their unique optical properties allow them to be used across the UV–vis-NIR spectrum tuned by their size, shape, and material. In addition to utility in enhanced spectroscopy and energy/charge transfer, the plasmon ...
    • 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 ...