Now showing items 323-342 of 476

    • Projected coupled cluster theory 

      Qiu, Yiheng; Henderson, Thomas M.; Zhao, Jinmo; Scuseria, Gustavo E. (2017)
      Coupled cluster theory is the method of choice for weakly correlated systems. But in the strongly correlated regime, it faces a symmetry dilemma, where it either completely fails to describe the system or has to artificially ...
    • Projected coupled cluster theory: Optimization of cluster amplitudes in the presence of symmetry projection 

      Qiu, Yiheng; Henderson, Thomas M.; Zhao, Jinmo; Scuseria, Gustavo E. (2018)
      Methods which aim at universal applicability must be able to describe both weak and strong electronic correlation with equal facility. Such methods are in short supply. The combination of symmetry projection for strong ...
    • Projected Hartree-Fock theory as a polynomial of particle-hole excitations and its combination with variational coupled cluster theory 

      Qiu, Yiheng; Henderson, Thomas M.; Scuseria, Gustavo E. (2017)
      Projected Hartree-Fockᅠtheoryᅠprovides an accurate description of many kinds of strong correlations but does not properly describe weakly correlated systems.ᅠCoupled clusterᅠtheory,ᅠin contrast, does the opposite. It ...
    • Projected Hartree–Fock theory 

      Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Tsuchimochi, Takashi; Scuseria, Gustavo E. (2012)
      Projected Hartree–Fock (PHF) theory has a long history in quantum chemistry. PHF is here understood as the variational determination of an N-electron broken symmetry Slater determinant that minimizes the energy of a projected ...
    • Proper and improper zero energy modes in Hartree-Fock theory and their relevance for symmetry breaking and restoration 

      Cui, Yao; Bulik, Ireneusz W.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Scuseria, Gustavo E. (2013)
      We study the spectra of the molecular orbital Hessian (stability matrix) and random-phase approximation (RPA) Hamiltonian of broken-symmetry Hartree-Fock solutions, focusing on zero eigenvalue modes. After all negative ...
    • 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 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 ...