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NEWS

See News archive for all news.

2010

• 21.01.  Submitted article: M. Buchowiecki and J. Vanicek, "Direct evaluation of the temperature dependence of the rate constant based on the quantum instanton approximation."

• 18.01.  Submitted article: T. Zimmermann and J. Vanicek, "Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene." 

2009

• 18.12.  Submitted article: T. Zimmermann, J. Ruppen, B. Li, and J. Vanicek:  "Efficient evaluation of the accuracy of molecular quantum dynamics on an approximate analytical or interpolated potential energy surface."

• 15.12. Submitted article: R. Marin and J. Vanicek: "Specificity of microRNA target predictions improved by RNA secondary structure calculations."

• 01.09. Our article "Efficient evaluation of accuracy of molecular quantum dynamics using dephasing representation" was the most downloaded scientific paper in the Journal of Chemical Physics in August 2009! See the announcement here.

2008

• 14.04. Version 10 of AMBER software suite has been released. Our contribution was the code for thermodynamic integration with respect to mass, and the section in the manual on isotope effects. The method is based on the AMBER implementation of Path Integral Molecular Dynamics and is useful for calculation of both equilibrium and kinetic isotope effects.

• 08.04. Our article "Suppression of immediate-early gene expression by herpesvirus-coded microRNAs: Implications for latency" was featured in the "In This Issue" section of the Proceedings of the National Academy of Sciences of the USA. See "Herpesvirus miRNAs control latency."

OPEN POSITIONS

• Master projects are available for the fall semester 2009.

• Ph.D. position in theoretical chemical physics.

PREPRINTS

SELECTED PUBLICATIONS

• T. Zimmermann and J. Vanicek. "Path integral evaluation of the equilibrium isotope effect in [1,5] sigmatropic hydrogen shift reactions".
Flash Informatique, 8/2009, 37 (2009).
[detailed record]

• B. Li, C. Mollica and J. Vanicek. "Efficient evaluation of accuracy of molecular quantum dynamics using dephasing representation".
Journal of Chemical Physics, 131, 041101 (2009).
[detailed record]

• T. Zimmermann and J. Vanicek. "Path integral evaluation of equilibrium isotope effects".
Journal of Chemical Physics 131, 024111 (2009).
[detailed record]

• E. Murphy, J. Vanicek, H. Robins, T. Shenk, and A. J. Levine. "Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: Implications for latency".
Proceedings of the National Academy of Sciences of the United States of America 105, 5453 (2008).
[detailed record]

• D.A. Case, T.A. Darden, T.E. Cheatham, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, M. Crowley, R.C. Walker, W. Zhang, K.M. Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvary, K.F. Wong, F. Paesani, J. Vanicek, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, and P.A. Kollman: AMBER 10. San Francisco , University of California (2008).
[detailed record]

• J. Vanicek and W.H. Miller. "Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene".
Journal of Chemical Physics 127, 114309 (2007).
[detailed record]

• J. Vanicek. "Dephasing representation of quantum fidelity for general pure and mixed states".
Physical Review E 73, 046204 (2006).
[detailed record]

• J. Vanicek, W.H. Miller, J.F. Castillo, and F.J. Aoiz: "Quantum-instanton evaluation of the kinetic isotope effects".
Journal of Chemical Physics 123, 054108 (2005).
[detailed record]

• Jiri Vanicek. "Dephasing representation: Employing the shadowing theorem to calculate quantum correlation functions".
Physical Review E 70, 055201 (2004).
[detailed record]

• J. Vanicek and E.J. Heller: "Semiclassical evaluation of quantum fidelity".
Physical Review E 68, 056208 (2003).
[detailed record]