The Experts below are selected from a list of 6609 Experts worldwide ranked by ideXlab platform
Stephen J Klippenstein - One of the best experts on this subject based on the ideXlab platform.
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variable reaction coordinate transition state theory analytic results and application to the c2h3 h c2h4 reaction
Journal of Chemical Physics, 2003Co-Authors: Yuri Georgievskii, Stephen J KlippensteinAbstract:A novel derivation is provided for the canonical, microcanonical, and energy E and total angular momentum J resolved reactive flux within the variable reaction coordinate transition state theory (VRC-TST) formalism. The use of an alternative representation for the reaction coordinate velocity yields a new expression for the kinematic factor which better illustrates its dependence on the Pivot Point location, and which can be straightforwardly evaluated. Also, the use of a geometric approach in place of an earlier algebraic one clarifies the derivation as does the use of Lagrange multiplier methodology for the analytic integration over the total angular momentum. Finally, a quaternion representation for the fragment and line-of-centers orientations is employed in place of the Euler angle or internal/external rotational coordinates used in prior studies. The result is an efficient, and particularly easy to implement, methodology for performing variable reaction coordinate transition state theory calculation...
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variable reaction coordinate transition state theory analytic results and application to the c2h3 h c2h4 reaction
Journal of Chemical Physics, 2003Co-Authors: Yuri Georgievskii, Stephen J KlippensteinAbstract:A novel derivation is provided for the canonical, microcanonical, and energy E and total angular momentum J resolved reactive flux within the variable reaction coordinate transition state theory (VRC-TST) formalism. The use of an alternative representation for the reaction coordinate velocity yields a new expression for the kinematic factor which better illustrates its dependence on the Pivot Point location, and which can be straightforwardly evaluated. Also, the use of a geometric approach in place of an earlier algebraic one clarifies the derivation as does the use of Lagrange multiplier methodology for the analytic integration over the total angular momentum. Finally, a quaternion representation for the fragment and line-of-centers orientations is employed in place of the Euler angle or internal/external rotational coordinates used in prior studies. The result is an efficient, and particularly easy to implement, methodology for performing variable reaction coordinate transition state theory calculation...
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kinetic isotope effects and variable reaction coordinates in barrierless recombination reactions
Journal of Physical Chemistry A, 2001Co-Authors: Craig A Taatjes, Stephen J KlippensteinAbstract:The factors affecting kinetic isotope effects in barrierless recombination reactions are considered from the perspective of variational transition state theory (VTST). Despite the broad application of VTST methods, a general consideration of kinetic isotope effect predictions of the theory has not previously been undertaken, especially for cases where changes in the internal structure and vibrational frequencies of the fragments (i.e., the conserved modes) can be assumed to be negligible. Use of the center-of-mass separation as the reaction coordinate in such a case entails some restriction on the range of kinetic isotope effects which can be accommodated. Larger effects are possible within a variable reaction coordinate implementation of transition state theory, and the predicted kinetic isotope effects are shown to be strongly dependent on the location of the Pivot Point. Illustrative model calculations demonstrate the feasibility of reproducing the experimentally observed kinetic isotope effects for th...
Darwin G Caldwell - One of the best experts on this subject based on the ideXlab platform.
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AwAS-II: A new Actuator with Adjustable Stiffness based on the novel principle of adaptable Pivot Point and variable lever ratio
2011 IEEE International Conference on Robotics and Automation, 2011Co-Authors: Amir Jafari, Nikolaos G Tsagarakis, Darwin G CaldwellAbstract:The Actuator with Adjustable Stiffness (AwAS) is an actuator which can independently control equilibrium position and stiffness by two motors. The first motor controls the equilibrium position while the second motor regulates the compliance. This paper describes the design and development of AwAS-II which is an improved version of the original realization. AwAS tuned the stiffness by controlling the location of the springs and adjusting its arm, length. Instead AwAS-II regulates the compliance by implementing a force amplifier based on a lever mechanism on which a Pivot Point can adjust the force amplification ratio from zero to infinitive. As in the first implementation, the actuator which is responsible for adjusting the stiffness in AwAS II is not working against the spring forces. Its displacement is perpendicular to the force generated by springs which makes changing the stiffness energetically efficient. As the force amplification ratio can theoretically change from zero to infinitive consequently the level of stiffness can tune from very soft to completely rigid. Because this range does not depends on the spring's rate and length of the lever, thus soft springs and small lever can be used which result in a lighter and more compact setup. Furthermore as the lever arm is shorter the time required for the stiffness regulation is smaller.
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A new variable stiffness actuator (CompAct-VSA): Design and modelling
IEEE International Conference on Intelligent Robots and Systems, 2011Co-Authors: Nikolaos G Tsagarakis, Irene Sardellitti, Darwin G CaldwellAbstract:This paper describes the design and modelling of a new variable stiffness actuator (CompAct-VSA). The principle of operation of CompAct-VSA is based on a lever arm mechanism with a continuously regulated Pivot Point. The proposed concept allows for the development of an actuation unit with a wide range of stiffness and a fast stiffness regulation response. The implementation of the actuator makes use of a cam shaped lever arm with a variable Pivot axis actuated by a rack and pinion transmission system. This realization results in a highly integrated and modular assembly. Size and weight are indeed an open issue in the VSAs design, which ultimately limit their implementation in multi-dof robotic systems. The paper introduces the mechanics, the principle of operation and the model of the actuator. Preliminary results are presented to demonstrate the fast stiffness regulation response and the wide range of stiffness achieved by the proposed CompAct-VSA design.
John A. Tainer - One of the best experts on this subject based on the ideXlab platform.
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structural basis for fen 1 substrate specificity and pcna mediated activation in dna replication and repair
Cell, 2004Co-Authors: Brian R Chapados, David J Hosfield, B Yelent, Binghui Shen, John A. TainerAbstract:Abstract Flap EndoNuclease-1 (FEN-1) and the processivity factor proliferating cell nuclear antigen (PCNA) are central to DNA replication and repair. To clarify the molecular basis of FEN-1 specificity and PCNA activation, we report here structures of FEN-1:DNA and PCNA:FEN-1-peptide complexes, along with fluorescence resonance energy transfer (FRET) and mutational results. FEN-1 binds the unpaired 3′ DNA end (3′ flap), opens and kinks the DNA, and promotes conformational closing of a flexible helical clamp to facilitate 5′ cleavage specificity. Ordering of unstructured C-terminal regions in FEN-1 and PCNA creates an intermolecular β sheet interface that directly links adjacent PCNA and DNA binding regions of FEN-1 and suggests how PCNA stimulates FEN-1 activity. The DNA and protein conformational changes, composite complex structures, FRET, and mutational results support enzyme-PCNA alignments and a kinked DNA Pivot Point that appear suitable to coordinate rotary handoffs of kinked DNA intermediates among enzymes localized by the three PCNA binding sites.
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structural basis for fen 1 substrate specificity and pcna mediated activation in dna replication and repair
Cell, 2004Co-Authors: Brian R Chapados, David J Hosfield, B Yelent, Binghui Shen, John A. TainerAbstract:Abstract Flap EndoNuclease-1 (FEN-1) and the processivity factor proliferating cell nuclear antigen (PCNA) are central to DNA replication and repair. To clarify the molecular basis of FEN-1 specificity and PCNA activation, we report here structures of FEN-1:DNA and PCNA:FEN-1-peptide complexes, along with fluorescence resonance energy transfer (FRET) and mutational results. FEN-1 binds the unpaired 3′ DNA end (3′ flap), opens and kinks the DNA, and promotes conformational closing of a flexible helical clamp to facilitate 5′ cleavage specificity. Ordering of unstructured C-terminal regions in FEN-1 and PCNA creates an intermolecular β sheet interface that directly links adjacent PCNA and DNA binding regions of FEN-1 and suggests how PCNA stimulates FEN-1 activity. The DNA and protein conformational changes, composite complex structures, FRET, and mutational results support enzyme-PCNA alignments and a kinked DNA Pivot Point that appear suitable to coordinate rotary handoffs of kinked DNA intermediates among enzymes localized by the three PCNA binding sites.
Raffaella Carloni - One of the best experts on this subject based on the ideXlab platform.
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the variable stiffness actuator vsaut ii mechanical design modeling and identification
IEEE-ASME Transactions on Mechatronics, 2014Co-Authors: Stefan S Groothuis, Giacomo Rusticelli, Andrea Zucchelli, Stefano Stramigioli, Raffaella CarloniAbstract:In this paper, the rotational variable stiffness actuator vsaUT-II is presented. This actuation system is characterized by the property that the apparent stiffness at the actuator output can be varied independently from its position. This behavior is realized by implementing a variable transmission ratio between the internal elastic elements and the actuator output, i.e., a lever arm with variable Pivot Point position. The Pivot Point is moved by a planetary gears mechanism, which acquires a straight motion from only rotations, thereby providing a low-friction transmission. The working principle details of the vsaUT-II are elaborated and the design is presented. The actuator dynamics are described by means of a lumped parameter model. The relevant parameters of the actuator are estimated and identified in the physical setup and measurements are used to validate both the design and the derived model.
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the mvsa ut a miniaturized differential mechanism for a continuous rotational variable stiffness actuator
IEEE International Conference on Biomedical Robotics and Biomechatronics, 2012Co-Authors: Matteo Fumagalli, Stefano Stramigioli, Eamon Barrett, Raffaella CarloniAbstract:In this paper, we present the mechanical design of the mVSA-UT, a miniaturized variable stiffness actuator. The apparent output stiffness of this innovative actuation system can be changed independently of the output position by varying the transmission ratio between the internal mechanical springs and the actuator output. The output stiffness can be tuned from zero to almost infinite by moving a Pivot Point along a lever arm. The mVSA-UT is actuated by means of two motors, connected in a differential configuration, which both work together to change the output stiffness and the output position. The output shaft can perform unbounded and continuous rotation. The design ensures high output torque capability, light weight and compact size to realize a multiple purpose actuation unit for a great variety of robotic and biomechatronic applications.
Judith Frydman - One of the best experts on this subject based on the ideXlab platform.
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the chaperonin tric cct associates with prefoldin through a conserved electrostatic interface essential for cellular proteostasis
Cell, 2019Co-Authors: Daniel R Gestaut, Soung Hun Roh, Grigore D Pintilie, Lukasz A Joachimiak, Alexander Leitner, Thomas Walzthoeni, Ruedi Aebersold, Wah Chiu, Judith FrydmanAbstract:Summary Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the chaperone prefoldin/GIMc (PFD), we integrate cryoelectron microscopy (cryo-EM), crosslinking-mass-spectrometry and biochemical and cellular approaches to elucidate the structural and functional interplay between TRiC/CCT and PFD. We find these hetero-oligomeric chaperones associate in a defined architecture, through a conserved interface of electrostatic contacts that serves as a Pivot Point for a TRiC-PFD conformational cycle. PFD alternates between an open “latched” conformation and a closed “engaged” conformation that aligns the PFD-TRiC substrate binding chambers. PFD can act after TRiC bound its substrates to enhance the rate and yield of the folding reaction, suppressing non-productive reaction cycles. Disrupting the TRiC-PFD interaction in vivo is strongly deleterious, leading to accumulation of amyloid aggregates. The supra-chaperone assembly formed by PFD and TRiC is essential to prevent toxic conformations and ensure effective cellular proteostasis.
