Rensselaer Polytechnic Institute

About: Rensselaer Polytechnic Institute is a education organization based out in Troy, New York, United States. It is known for research contribution in the topics: Terahertz radiation & Population. The organization has 19024 authors who have published 39922 publications receiving 1414699 citations. The organization is also known as: RPI & Rensselaer Institute.

Equilibrium Study of Protein Denaturation by Urea

Abstract: Though urea is commonly used to denature proteins, the molecular mechanism of its denaturing ability is still a subject of considerable debate. Previous molecular dynamics simulation studies have sought to elucidate the mechanism of urea denaturation by focusing on the pathway of denaturation rather than examining the effect of urea on the folding/unfolding equilibrium, which is commonly measured in experiment. Here we report the reversible folding/unfolding equilibrium of Trp-cage miniprotein in the presence of urea, over a broad range of urea concentrations, using all-atom Replica exchange MD simulations. The simulations capture the experimentally observed linear dependence of unfolding free energy on urea concentration. We find that the denaturation is driven by favorable direct interaction of urea with the protein through both electrostatic and van der Waals forces and quantify their contribution. Though the magnitude of direct electrostatic interaction of urea is larger than van der Waals, the difference between unfolded and folded ensembles is dominated by the van der Waals interaction. We also find that hydrogen bonding of urea to the peptide backbone does not play a dominant role in denaturation. The unfolded ensemble sampled depends on urea concentration, with greater urea concentration favoring conformations with greater solvent exposure. The m-value is predicted to increase with temperature and more strongly so with pressure.

Block kinematics of the Pacific-North America plate boundary in the southwestern United States from inversion of GPS, seismological, and geologic data

Abstract: [1] The active deformation of the southwestern United States (30°–41°N) is represented by a finite number of rotating, elastic-plastic spherical caps. GPS-derived horizontal velocities, geologic fault slip rates, transform fault azimuths, and earthquake-derived fault slip vector azimuths are inverted for block angular velocities, creep on block-bounding faults, permanent strain rates within the blocks, and the rotations of 11 published GPS velocity fields into to a common North American reference frame. GPS velocities are considered to be a combination of rigid block rotations, recoverable elastic strain rates resulting from friction on block-bounding faults, and nonrecoverable strain rates resulting from slip on faults within the blocks. The resulting Pacific–North America angular velocity is similar to some published estimates and satisfies transform azimuths and one spreading rate in the Gulf of California, earthquake slip vectors in the Gulf of California and Alaska, and GPS velocities along coastal California and within the Pacific Basin. Published fault slip rates are satisfied except in the southern Mojave Desert where the motion of the Mohave block relative to North America is faster than can be explained by mapped faults. The largest blocks, the Sierra Nevada–Great Valley and the eastern Basin and Range, show permanent strain rates, after removing elastic strain, of only a few nanostrain per year, demonstrating approximately rigid behavior. Observed horizontal strain rates correlate strongly with predicted strain rates from known faults suggesting that the short-term strains evident in GPS velocities are largely elastic. In only about 20% of the region is distributed deformation needed to match the data, indicating that a plate tectonic style description of the deformation of the western United States is plausible. Most blocks rotate about vertical axes at approximately the same rate as the Pacific (relative to North America), suggesting that locally, spin rates are communicated from block to block, arguing against both floating block and ball-bearing mechanisms of block rotation. The similarities of the blocks' spin rates to that of the Pacific suggests that the Pacific strongly influences their motions through edge tractions. However, it is shown that the blocks cannot rotate about the Pacific–North America pole without spinning counter to the sense of Pacific–North America shear. Unlike some other broad plate boundaries, in the western United States, vertical axis rotations take up very little of the slip rate budget across the region.

Electrocorticography-based brain computer Interface-the seattle experience

Abstract: Electrocorticography (ECoG) has been demonstrated to be an effective modality as a platform for brain-computer interfaces (BCIs). Through our experience with ten subjects, we further demonstrate evidence to support the power and flexibility of this signal for BCI usage. In a subset of four patients, closed-loop BCI experiments were attempted with the patient receiving online feedback that consisted of one-dimensional cursor movement controlled by ECoG features that had shown correlation with various real and imagined motor and speech tasks. All four achieved control, with final target accuracies between 73%-100%. We assess the methods for achieving control and the manner in which enhancing online control can be accomplished by rescreening during online tasks. Additionally, we assess the relevant issues of the current experimental paradigm in light of their clinical constraints.