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Echeverria C.,Chemical Physics Theory Group | Echeverria C.,University of Los Andes, Venezuela | Kapral R.,Chemical Physics Theory Group
Physical Chemistry Chemical Physics | Year: 2012

The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding. © 2012 the Owner Societies. Source


Elran Y.,Chemical Physics Theory Group | Elran Y.,Weizmann Institute of Science | Brumer P.,Chemical Physics Theory Group
Journal of Chemical Physics | Year: 2013

Vibrational decoherence of a "breathing sphere" oscillator in a thermal Lennard-Jones bath is examined using a classical analog approach. The equivalence between this approach and the linearized semiclassical initial value representation (IVR) is established and the method is exploited to produce a useful computational strategy that can efficiently evaluate the time dependence of the decoherence in these systems. A comparison between Harmonic and Morse "breathing sphere" models is presented and the rate of decoherence is found to depend on the choice of model, the initial state of the oscillator, the initial conditions of the bath (temperature, density), and the choice of quantity measuring the decoherence rate. The results are used to examine the utility of the Caldeira-Leggett model in this realistic system. © 2013 AIP Publishing LLC. Source


Yu C.X.,Chemical Physics Theory Group | Wu L.-A.,University of the Basque Country | Segal D.,Chemical Physics Theory Group
Physics Letters, Section A: General, Atomic and Solid State Physics | Year: 2010

We consider quantum heat flow in two-terminal junctions and inquire on the connection between the transport mechanism and the junction functionality. Using simple models, we demonstrate that the violation of the Landauer behavior in asymmetric junctions does not necessarily imply the onset of thermal rectification. We also demonstrate through a simple example that a spatial inhomogeneity of the energy spectra is not a necessary condition for thermal rectification. © 2009 Elsevier B.V. All rights reserved. Source


Franco I.,Chemical Physics Theory Group | Spanner M.,Chemical Physics Theory Group | Brumer P.,Chemical Physics Theory Group
Chemical Physics | Year: 2010

The analogy between Young's double-slit experiment with matter and laser driven coherent control schemes is investigated, and shown to be limited. To do so, a general decomposition of observables in the Heisenberg picture into direct terms and interference contributions is introduced, and formal quantum-classical correspondence arguments in the Heisenberg picture are employed to define classical analogs of quantum interference terms. While the classical interference contributions in the double-slit experiment are shown to be zero, they can be nonzero in laser driven coherent control schemes and lead to laser control in the classical limit. This classical limit is interpreted in terms of nonlinear response theory arguments. © 2010 Elsevier B.V. All rights reserved. Source

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