Arthur La Porta
Cornell University
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Publication
Featured researches published by Arthur La Porta.
Proceedings of the National Academy of Sciences of the United States of America | 2002
Karen Adelman; Arthur La Porta; Thomas J. Santangelo; John T. Lis; Jeffrey W. Roberts; Michelle D. Wang
By using single-molecule measurements, we demonstrate that the elongation kinetics of individual Escherichia coli RNA polymerase molecules are remarkably homogeneous. We find no evidence of distinct elongation states among RNA polymerases. Instead, the observed heterogeneity in transcription rates results from statistical variation in the frequency and duration of pausing. When transcribing a gene without strong pause sites, RNA polymerase molecules display transient pauses that are distributed randomly in both time and distance. Transitions between the active elongation mode and the paused state are instantaneous within the resolution of our measurements (<1 s). This elongation behavior is compared with that of a mutant RNA polymerase that pauses more frequently and elongates more slowly than wild type.
Review of Scientific Instruments | 2001
Greg Voth; Arthur La Porta; Alice M. Crawford; Eberhard Bodenschatz; Curt Ward; J. P. Alexander
We describe a high speed imaging system that is used to track tracer particles in highly turbulent flows. The system uses silicon strip detectors designed for high energy physics experiments and is capable of reading two detectors at a frame rate of 70 kHz. Each detector contains 512 strips and measures a one-dimensional projection of the light striking it. The position measurements from this system have a dynamic range of 6400:1. Extensions to higher frame rates and more detectors are possible. We describe the detectors, readout system, supporting systems, and give an evaluation of the measurement accuracy.
Physical Review E | 2013
Arthur La Porta; Natalia A. Denesyuk; Michel de Messieres
In experiments and in simulations, the free energy of a state of a system can be determined from the probability that the state is occupied. However, it is often necessary to impose a biasing potential on the system so that high energy states are sampled with sufficient frequency. The unbiased energy is typically obtained from the data using the weighted histogram analysis method (WHAM). Here we present differential energy surface analysis (DESA), in which the gradient of the energy surface, dE/dx, is extracted from data taken with a series of harmonic biasing potentials. It is shown that DESA produces a maximum likelihood estimate of the folding landscape gradient. DESA is demonstrated by analyzing data from a simulated system as well as data from a single-molecule unfolding experiment in which the end-to-end distance of a DNA hairpin is measured. It is shown that the energy surface obtained from DESA is indistinguishable from the energy surface obtained when WHAM is applied to the same data. Two criteria are defined which indicate whether the DESA results are self-consistent. It is found that these criteria can detect a situation where the energy is not a single-valued function of the measured reaction coordinate. The criteria were found to be satisfied for the experimental data analyzed, confirming that end-to-end distance is a good reaction coordinate for the experimental system. The combination of DESA and the optical trap assay in which a structure is disrupted under harmonic constraint facilitates an extremely accurate measurement of the folding energy surface.
Physical Review Letters | 2004
Arthur La Porta; Michelle D. Wang
Molecular Cell | 2004
Karen Adelman; Julia Yuzenkova; Arthur La Porta; Nikolay Zenkin; Jookyung Lee; John T. Lis; Sergei Borukhov; Michelle D. Wang; Konstantin Severinov
Physical Review Letters | 2012
Michel de Messieres; Jen-Chien Chang; Barbara Brawn-Cinani; Arthur La Porta
Archive | 2001
Alice M. Crawford; Arthur La Porta; Eberhard Bodenschatz; James C. Alexander
Biophysics | 2013
Jen-Chien Chang; Michel de Messieres; Arthur La Porta
Biophysical Journal | 2012
Michel de Messieres; Jen-Chien Chang; Ashton T. Belew; Arturas Meskauskas; Jonathan D. Dinman; Arthur La Porta
Archive | 2001
Arthur La Porta; Alice M. Crawford; Gregory A. Voth; Eberhard Bodenschatz; James C. Alexander