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The Journal of Physical Chemistry B, ISSN 1089-5647, 05/2008, Volume 112, Issue 20, pp. 6304 - 6308
The lowest few electronic excitations of a π-stacked adenine dimer in its B-DNA geometry are investigated, in the gas phase and in a water cluster, using a... 
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 2008, Volume 129, Issue 3, p. 034107
We present benchmark calculations using several long-range-corrected (LRC) density functionals, in which Hartree-Fock exchange is incorporated asymptotically... 
EXCITATION-ENERGIES | APPROXIMATION | CLUSTERS | THERMOCHEMISTRY | PBE0 MODEL | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | EXCHANGE | LARGE MOLECULES
Journal Article
Annual Review of Physical Chemistry, ISSN 0066-426X, 04/2013, Volume 64, Issue 1, pp. 295 - 316
The long-timescale dynamics of macromolecular systems can be oftentimes viewed as a reaction connecting metastable states of the system. In the past decade,... 
Molecular dynamics | Reaction rate | Path sampling | Machine learning | ENSEMBLE | MOLECULAR-DYNAMICS | CHEMISTRY, PHYSICAL | path sampling | reaction rate | TRANSITION-STATES | machine learning | molecular dynamics | SIMULATION | MOTIONS | FREE-ENERGY LANDSCAPES | STRING METHOD | RATE CONSTANTS | CONFIGURATIONAL ENTROPY | EFFICIENT | Chemical reactions | Chemistry, Analytic | Research | Methods
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 02/2009, Volume 130, Issue 5, pp. 054112 - 054112-8
We introduce a hybrid density functional that asymptotically incorporates full Hartree-Fock exchange, based on the long-range-corrected exchange-hole model of... 
HF calculations | SUITE | ground states | THERMOCHEMICAL KINETICS | GENERALIZED-GRADIENT-APPROXIMATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | charge transfer states | CHEMISTRY, PHYSICAL | EXCHANGE-CORRELATION FUNCTIONALS | MOLECULES | POLARIZABILITIES | CLUSTERS | excited states | density functional theory | organic compounds | OPERATORS | TDDFT
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 03/2011, Volume 134, Issue 12, pp. 124116 - 124116-11
We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed... 
LAPLACIAN | DEPENDENT DIFFUSION | STRUCTURE DEFINITION | REDUCTION | FREE-ENERGY LANDSCAPES | HARMONIC-ANALYSIS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | REPRESENTATION | CHEMISTRY, PHYSICAL | TRANSITION-STATE | NONNATIVE INTERACTIONS | GEOMETRIC DIFFUSIONS
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 10/2013, Volume 117, Issue 42, p. 12769
Journal Article
Journal of Physical Chemistry A, ISSN 1089-5639, 10/2013, Volume 117, Issue 42, p. 12769
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 10/2013, Volume 117, Issue 42, pp. 12769 - 12776
The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular... 
PATHWAYS | CHEMISTRY, PHYSICAL | SIMULATIONS | REDUCTION | FREE-ENERGY | Thermodynamics | Temperature | Hydrogen Bonding | Alanine - chemistry | Diffusion | Dipeptides - chemistry | Molecular Dynamics Simulation | Protein Folding | Molecular dynamics | Exploration | Sampling | Dynamical systems | Gain | Standards | Free energy | molecular dynamics | umbrella sampling | diffusion map
Journal Article
by Shao, Yihan and Gan, Zhengting and Epifanovsky, Evgeny and Gilbert, Andrew T.B and Wormit, Michael and Kussmann, Joerg and Lange, Adrian W and Behn, Andrew and Deng, Jia and Feng, Xintian and Ghosh, Debashree and Goldey, Matthew and Horn, Paul R and Jacobson, Leif D and Kaliman, Ilya and Khaliullin, Rustam Z and Kuś, Tomasz and Landau, Arie and Liu, Jie and Proynov, Emil I and Rhee, Young Min and Richard, Ryan M and Rohrdanz, Mary A and Steele, Ryan P and Sundstrom, Eric J and Woodcock, H. Lee and Zimmerman, Paul M and Zuev, Dmitry and Albrecht, Ben and Alguire, Ethan and Austin, Brian and Beran, Gregory J. O and Bernard, Yves A and Berquist, Eric and Brandhorst, Kai and Bravaya, Ksenia B and Brown, Shawn T and Casanova, David and Chang, Chun-Min and Chen, Yunqing and Chien, Siu Hung and Closser, Kristina D and Crittenden, Deborah L and Diedenhofen, Michael and DiStasio, Robert A and Do, Hainam and Dutoi, Anthony D and Edgar, Richard G and Fatehi, Shervin and Fusti-Molnar, Laszlo and Ghysels, An and Golubeva-Zadorozhnaya, Anna and Gomes, Joseph and Hanson-Heine, Magnus W.D and Harbach, Philipp H.P and Hauser, Andreas W and Hohenstein, Edward G and Holden, Zachary C and Jagau, Thomas-C and Ji, Hyunjun and Kaduk, Benjamin and Khistyaev, Kirill and Kim, Jaehoon and Kim, Jihan and King, Rollin A and Klunzinger, Phil and Kosenkov, Dmytro and Kowalczyk, Tim and Krauter, Caroline M and Lao, Ka Un and Laurent, Adèle D and Lawler, Keith V and Levchenko, Sergey V and Lin, Ching Yeh and Liu, Fenglai and Livshits, Ester and Lochan, Rohini C and Luenser, Arne and Manohar, Prashant and Manzer, Samuel F and Mao, Shan-Ping and Mardirossian, Narbe and Marenich, Aleksandr V and Maurer, Simon A and Mayhall, Nicholas J and Neuscamman, Eric and Oana, C. Melania and Olivares-Amaya, Roberto and O'Neill, Darragh P and Parkhill, John A and Perrine, Trilisa M and Peverati, Roberto and Prociuk, Alexander and Rehn, Dirk R and Rosta, Edina and Russ, Nicholas J and Sharada, Shaama M and Sharma, Sandeep and Small, David W and Sodt, Alexander and ...
Molecular Physics, ISSN 0026-8976, 01/2015, Volume 113, Issue 2, pp. 184 - 215
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 05/2008, Volume 112, Issue 20, pp. 6304 - 6308
The lowest few electronic excitations of a pi-stacked adenine dimer in its B-DNA geometry are investigated, in the gas phase and in a water cluster, using a... 
EXCITATION-ENERGIES | BASE STACKING | FLUORESCENCE | ELECTRONIC-TRANSITIONS | DNA | DOUBLE HELICES | DYNAMICS | CHEMISTRY, PHYSICAL | MODEL | 2-AMINOPURINE | EXCHANGE | Models, Molecular | Adenine - chemistry | Dimerization
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 04/2011, Volume 134, Issue 14, pp. 144109 - 144109-8
A recent study on the dynamics of polymer reversal inside a nanopore by Huang and Makarov [ J. Chem. Phys. 128 , 114903 ( 2008 )] 10.1063/1.2890006... 
LAPLACIAN | TRANSLOCATION | TRANSPORT | FORCE | DNA | PORE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | REPRESENTATION | DYNAMICS | CHEMISTRY, PHYSICAL | SIMULATIONS | Thermodynamics | Algorithms | Time Factors | Molecular Conformation | Polymers - chemistry | Kinetics | Diffusion | Nanopores | Chemistry, Physical - methods | Molecular Dynamics Simulation
Journal Article
Physical Chemistry Chemical Physics, ISSN 1463-9076, 5/2012, Volume 14, Issue 21, pp. 7679 - 7699
Journal Article
PLoS Computational Biology, ISSN 1553-734X, 10/2014, Volume 10, Issue 10
  The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition... 
Proteins | Fourier transforms | Experiments | Methods
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 11/2011, Volume 115, Issue 44, pp. 13065 - 13074
Journal Article