science

van Gunsteren's group
Canuto's group
CECM molecular sciences undergrad program (portuguese)

daniel trzesniak

academic background
PhD in Chemistry
Swiss Federal Institute of Technology
Sep/2002 - Jun/2006
MSc in Physics
University of São Paulo
Mar/2000 - Apr/2002
BSc in Molecular Sciences
University of São Paulo
Jul/1996 - Dec/1999


theses

  1. "Interplay between computer simulation and experimental data in physical chemistry and structural biology: testing, interpretation and prediction."
    D. Trzesniak - Advisor: W. F. van Gunsteren
    PhD - Swiss Federal Institute of Technology - Jun/2006

  2. "Quantum Modeling of Enzymatic Inhibitors."
    D. Trzesniak - Advisor: S. Canuto
    MSc - University of São Paulo - Apr/2002

publications

articles

  1. "Exact Distances and Internal Dynamics of Perdeuterated Ubiquitin from NOE Buildups"
    B. Vögeli et al.
    J AM CHEM SOC, 131: 17215-17225 2009

  2. "On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models"
    M. Winger et al.
    PHYS CHEM CHEM PHYS, 11: 1934-1941 2009

  3. "Vaporization, solvation and phase-partitioning thermodynamics of aliphatic hydrocarbons: A molecular dynamics study comparing coarse-grained and atomic-level simulation models"
    R. Baron et al.
    CHEMPHYSCHEM, 8: 452-461 2007 

  4. "Analysis of neo-pentane-urea pair potentials of mean force in aqueous urea"
    D. Trzesniak, N. F. A. van der Vegt, W. F. van Gunsteren
    MOL PHYS, 105: 33-39 2007 

  5. "A comparison of methods to compute a potential of mean force"
    D. Trzesniak, A-P. E. Kunz, W. F. van Gunsteren
    CHEMPHYSCHEM, 8: 162-169 2007 

  6. "Simulation of an all-β3-icosapeptide containing the twenty proteinogenic side chains: effect of temperature, pH, counter-ions, solvent and force field on helix stability"
    D. Trzesniak, B. Jaun, R. I. Mathad, W. F. van Gunsteren
    BIOPOLYMERS, 83: 636-645 2006

  7. "Pathway dependence of the efficiency of calculating free energy and entropy of solute-solute association in water"
    D. Trzesniak, W. F. van Gunsteren
    CHEM PHYS, 330: 410-416 2006 

  8. "Catalytic mechanism of Cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution data"
    D. Trzesniak, W. F. van Gunsteren
    PROTEIN SCI, 15: 2544-2551 2006 

  9. "Enthalpy-entropy compensation in the effects of urea on hydrophobic interactions"
    N. F. A. van der Vegt, M-E. Lee, D. Trzesniak, W. F. van Gunsteren
    J PHYS CHEM B, 110: 12852-12855 2006 

  10. "A protein under pressure: molecular dynamics simulation of the Arc Repressor"
    D. Trzesniak, R. D. Lins, W. F. van Gunsteren
    PROTEINS, 65: 136-144 2006 

  11. "Biomolecular modeling: goals, problems, perspectives"
    W. F. van Gunsteren et al.
    ANGEW CHEMIE INT ED, 45: 4064-4092 2006 

  12. "The GROMOS software for biomolecular simulation" GROMOS05"
    M. Christen et al.
    J COMP CHEM, 26: 1719-1751 2005 

  13. "Interpreting NMR data for β-peptides using molecular dynamics simulations"
    D. Trzesniak, A. Glättli, B. Jaun, W. F. van Gunsteren
    J AM CHEM SOC, 127: 14320-14329 2005 

  14. "Computer simulation studies on the solvation of aliphatic hydrocarbons in 6.9 M aqueous urea solution"
    D. Trzesniak, N. F. A. van der Vegt, W. F. van Gunsteren
    PHYS CHEM CHEM PHYS, 6: 697-702 2004 

  15. "Energy-entropy compensation in the transfer of non-polar solutes from water to co-solvent/water mixtures"
    N. F. A. van der Vegt, D. Trzesniak, B. Kasumaj, W. F. van Gunsteren
    CHEMPHYSCHEM, 5: 144-147 2004
    CHEMPHYSCHEM, 6: 1010-1010 2005

  16. "New developments in Monte Carlo/quantum mechanics methodology. The solvatochromism of β-carotene in different solvents"
    S. Canuto, K Coutinho, D Trzesniak
    ADV QUANTUM CHEM, 41:161-183 2002 

  17. "Quantum chemical studies of the spectroscopic properties of the E-64 protease inhibitor"
    D. Trzesniak, A. C. F. Caires, P. C. Almeida, S. Canuto
    J MOL STRUC-THEOCHEM, 585:129-141 2002

book chapters

  1. "Analysis of the driving forces for biomolecular solvation and association"
    W. F. van Gunsteren et al.
    in Protein Folding and Drug Design, International School of Physics "Enrico Fermi", 165: 177 (2007), ed. R.A. Broglia, L. Serrano and  G. Tiana, IOS Press, Amsterdam - SIF

  2. "van der Waals interaction probed by solvatochromic shifts"
    S. Canuto, D Trzesniak, K Coutinho
    in Current Developments in Atomic, Molecular and Chemical Physics with Applications, 17: 127 (2002), ed. M. Mohan, Kluwer Academic Publishers