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Finding transition pathways using the string method with swarms of trajectories.
An approach to find transition pathways in complex systems is presented. The method, which is related to the string method in collective variables of Maragliano et al. (J. Chem. Phys. 2006, 125,Expand
Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix.
The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD)Expand
Quantitative bounds for Markov chain convergence: Wasserstein and total variation distances
We present a framework for obtaining explicit bounds on the rate of convergence to equilibrium of a Markov chain on a general state space, with respect to both total variation and WassersteinExpand
Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations.
Multifrequency electron spin resonance (ESR) spectra provide a wealth of structural and dynamic information about the local environment of the spin label and, indirectly, about the spin-labeledExpand
Liquid state DNP using a 260 GHz high power gyrotron.
Dynamic nuclear polarization (DNP) at high magnetic fields (9.2 T, 400 MHz (1)H NMR frequency) requires high microwave power sources to achieve saturation of the EPR transitions. Here we describe theExpand
PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure.
Pulsed electron double resonance (PELDOR) spectroscopy reveals a prearranged tertiary structure of the 27 nucleotides long engineered neomycin-responsive riboswitch. Measured distances between spinExpand
Computation of DNP coupling factors of a nitroxide radical in toluene: seamless combination of MD simulations and analytical calculations.
  • Deniz Sezer
  • Chemistry, Medicine
  • Physical chemistry chemical physics : PCCP
  • 14 January 2013
Dynamic nuclear polarization (DNP) employs paramagnetic species to increase the NMR signal of nuclear spins. In liquids, the efficiency of the effect depends on the strength of the interactionExpand
Rationalizing Overhauser DNP of nitroxide radicals in water through MD simulations.
  • Deniz Sezer
  • Chemistry, Medicine
  • Physical chemistry chemical physics : PCCP
  • 21 January 2014
The recently introduced methodology (Sezer, Phys. Chem. Chem. Phys., 2013, 15, 526) for calculating dynamic nuclear polarization (DNP) coupling factors through synergistic use of molecular dynamicsExpand
Dynamic nuclear polarization coupling factors calculated from molecular dynamics simulations of a nitroxide radical in water.
The magnetic resonance signal obtained from nuclear spins is strongly affected by the presence of nearby electronic spins. This effect finds application in biomedical imaging and structuralExpand
Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories.
Simulating electron spin resonance spectra of nitroxide spin labels from motional models is necessary for the quantitative analysis of experimental spectra. We present a framework for modeling theExpand
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