Now showing items 343-362 of 496

    • Protein Folding and Structure Prediction from the Ground Up II: AWSEM for a/ß Proteins 

      Chen, M.; Lin, X.; Lu, W.; Onuchic, J.; Wolynes, P.G. (2016)
      The atomistic associative memory, water mediated, structure and energy model (AAWSEM) is an efficient coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases ...
    • Protein Folding and structure Prediction from the Ground Up: The Atomistic Associative Memory Structure and Energy Model (AAWSEM) 

      Chen, M.; Lin, Z.; Zheng, W.; Onuchic, J.N.; Wolynes, P.G. (2016)
      The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically ...
    • Protein Frustratometer 2: A tool to localize energetic frustration in protein molecules now with electrostatics 

      Gonzalo, P.; Schafer, N.; Radusky, L.; Tsai, M.; Gusovsky, A. B.; Wolynes, P.G.; Ferreiro, D. (2016)
      The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing ...
    • Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics 

      Parra, R. Gonzalo; Schafer, Nicholas P.; Radusky, Leandro G.; Tsai, Min-Yeh; Guzovsky, A. Brenda; Wolynes, Peter G.; Ferreiro, Diego U. (2016)
      The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing ...
    • Protein search for multiple targets on DNA 

      Lange, Martin; Kochugaeva, Maria; Kolomeisky, Anatoly B. (2015)
      Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A ...
    • Quantitative analysis of gas phase molecular constituents using frequency-modulated rotational spectroscopy 

      Lou, Minghe; Swearer, Dayne F.; Gottheim, Samuel; Phillips, Dane J.; Simmons, Jay G. Jr.; Halas, Naomi J.; Everitt, Henry O. (2019)
      Rotational spectroscopy has been used for decades for virtually unambiguous identification of gas phase molecular species, but it has rarely been used for the quantitative analysis of molecular concentrations. Challenges ...
    • Quantitative analysis of gas phase molecular constituents using frequency-modulated rotational spectroscopy 

      Lou, Minghe; Swearer, Dayne F.; Gottheim, Samuel; Phillips, Dane J.; Simmons, Jay G.; Halas, Naomi J.; Everitt, Henry O. (2019)
      Rotational spectroscopy has been used for decades for virtually unambiguous identification of gas phase molecular species, but it has rarely been used for the quantitative analysis of molecular concentrations. Challenges ...
    • Quantitative comparison of adaptive sampling methods for protein dynamics 

      Hruska, Eugen; Abella, Jayvee R.; Nüske, Feliks; Kavraki, Lydia E.; Clementi, Cecilia (2018)
      Adaptive sampling methods, often used in combination with Markov state models, are becoming increasingly popular for speeding up rare events in simulation such as molecular dynamics (MD) without biasing the system dynamics. ...
    • Quasiparticle coupled cluster theory for pairing interactions 

      Henderson, Thomas M.; Scuseria, Gustavo E.; Dukelsky, Jorge; Signoracci, Angelo; Duguet, Thomas (2014)
      We present an extension of the pair coupled cluster doubles (p-CCD) method to quasiparticles and apply it to the attractive pairing Hamiltonian. Near the transition point where number symmetry gets spontaneously broken, ...
    • RACIPE: a computational tool for modeling gene regulatory circuits using randomization 

      Huang, Bin; Jia, Dongya; Feng, Jingchen; Levine, Herbert; Onuchic, José N.; Lu, Mingyang (2018)
      BACKGROUND: One of the major challenges in traditional mathematical modeling of gene regulatory circuits is the insufficient knowledge of kinetic parameters. These parameters are often inferred from existing experimental ...
    • Range-Separated Brueckner Coupled Cluster Doubles Theory 

      Shepherd, James J.; Henderson, Thomas M.; Scuseria, Gustavo E. (2014)
      We introduce a range-separation approximation to coupled cluster doubles (CCD) theory that successfully overcomes limitations of regular CCD when applied to the uniform electron gas. We combine the short-range ladder channel ...
    • Rapid Calculation of Molecular Kinetics Using Compressed Sensing 

      Litzinger, Florian; Boninsegna, Lorenzo; Wu, Hao; Nüske, Feliks; Patel, Raajen; Baraniuk, Richard; Noé, Frank; Clementi, Cecilia (2018)
      Recent methods for the analysis of molecular kinetics from massive molecular dynamics (MD) data rely on the solution of very large eigenvalue problems. Here we build upon recent results from the field of compressed sensing ...
    • Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics 

      Zheng, Wenwei; Rohrdanz, Mary A.; Clementi, Cecilia (2013)
      The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and ...
    • Rapid heteroatom transfer to arylmetals utilizing multifunctional reagent scaffolds 

      Gao, Hongyin; Zhou, Zhe; Kwon, Doo-Hyun; Coombs, James; Jones, Steven; Behnke, Nicole Erin; Ess, Daniel H.; Kürti, László (2016)
      Arylmetals are highly valuable carbon nucleophiles that are readily and inexpensively prepared from aryl halides or arenes and widely used on both laboratory and industrial scales to react directly with a wide range of ...
    • Reader domain specificity and lysine demethylase-4 family function 

      Su, Zhangli; Wang, Fengbin; Lee, Jin-Hee; Stephens, Kimberly E.; Papazyan, Romeo; Voronina, Ekaterina; Krautkramer, Kimberly A.; Raman, Ana; Thorpe, Jeremy J.; Boersma, Melissa D.; Kuznetsov, Vyacheslav I.; Miller, Mitchell D.; Taverna, Sean D.; Phillips, George N. Jr.; Denu, John M. (2016)
      The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an ...
    • Rebar Graphene 

      Yan, Zheng; Peng, Zhiwei; Casillas, Gilberto; Lin, Jian; Xiang, Changsheng; Zhou, Haiqing; Yang, Yang; Ruan, Gedeng; Raji, Abdul-Rahman O.; Samuel, Errol L.G.; Hauge, Robert H.; Yacaman, Miguel Jose; Tour, James M. (2014)
      As the cylindrical sp2-bonded carbon allotrope, carbon nanotubes (CNTs) have been widely used to reinforce bulk materials such as polymers, ceramics, and metals. However, both the concept demonstration and the fundamental ...
    • Rebar Graphene from Functionalized Boron Nitride Nanotubes 

      Li, Yilun; Peng, Zhiwei; Larios, Eduardo; Wang, Gunuk; Lin, Jian; Yan, Zheng; Ruiz-Zepeda, Francisco; José-Yacamán, Miguel; Tour, James M. (2015)
      The synthesis of rebar graphene on Cu substrates is described using functionalized boron nitride nanotubes (BNNTs) that were annealed or subjected to chemical vapor deposition (CVD) growth of graphene. Characterization ...
    • Recoupling the singlet- and triplet-pairing channels in single-reference coupled cluster theory 

      Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E. (2016)
      It is well known that single-reference coupled cluster theory truncated to low orders of excitations gives the right answer for the right reason when systems are dominated by dynamical or weak correlation. Static or strong ...
    • Redox-dependent gating of VDAC by mitoNEET 

      Lipper, Colin H.; Stofleth, Jason T.; Bai, Fang; Sohn, Yang-Sung; Roy, Susmita; Mittler, Ron; Nechushtai, Rachel; Onuchic, José N.; Jennings, Patricia A. (2019)
      MitoNEET is an outer mitochondrial membrane protein essential for sensing and regulation of iron and reactive oxygen species (ROS) homeostasis. It is a key player in multiple human maladies including diabetes, cancer, ...
    • Reduction Kinetics of the Nanocluster [HxPMo12O40⊂H4Mo72Fe30(O2CMe)15O254(H2O)98-y(EtOH)y] 

      Esquenazi, Gibran L.; Barron, Andrew R. (2018)
      The reduction of the molecular iron-molybdenum-nanocluster, [HxPMo12O40⊂H4Mo72Fe30(O2CMe)15O254(H2O)98-y(EtOH)y](FeMoC), was studied using model free isoconversional methods. The reduction kinetics were evaluated using the ...