Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\gamma$ and the catalytic proton moving more than 0.5 \AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc

Structurally specific thermal fluctuations identify functional sites for DNA transcription

We report results showing that thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating both viral and bacterial DNA gene promoter segments, we found that the most probable opening occurs at the transcription start site. Minor openings appear to be related to other regulatory sites. Our results suggest that coherent thermal fluctuations play an important role in the initiation of transcription. Essential elements of the dynamics, in addition to sequence specificity, are nonlinearity and entropy, provided by local base-pair constraints

Heat exchange between two interacting nanoparticles beyond the fluctuation-dissipation regime

We show that the observed non-monotonic behavior of the thermal conductance between two nanoparticles when they are brought into contact is originated by an intricate phase space dynamics. Here it is assumed that this dynamics results from the thermally activated jumping through a rough energy landscape. A hierarchy of relaxation times plays the key role in the description of this complex phase space behaviour. Our theory enables us to analyze the heat transfer just before and at the moment of contact.Comment: 4 pages, 1 figure, approved for publication in Physical Review Letter

Hysteretic Optimization For Spin Glasses

The recently proposed Hysteretic Optimization (HO) procedure is applied to the 1D Ising spin chain with long range interactions. To study its effectiveness, the quality of ground state energies found as a function of the distance dependence exponent, $\sigma$, is assessed. It is found that the transition from an infinite-range to a long-range interaction at $\sigma=0.5$ is accompanied by a sharp decrease in the performance . The transition is signaled by a change in the scaling behavior of the average avalanche size observed during the hysteresis process. This indicates that HO requires the system to be infinite-range, with a high degree of interconnectivity between variables leading to large avalanches, in order to function properly. An analysis of the way auto-correlations evolve during the optimization procedure confirm that the search of phase space is less efficient, with the system becoming effectively stuck in suboptimal configurations much earlier. These observations explain the poor performance that HO obtained for the Edwards-Anderson spin glass on finite-dimensional lattices, and suggest that its usefulness might be limited in many combinatorial optimization problems.Comment: 6 pages, 9 figures. To appear in JSTAT. Author website: http://www.bgoncalves.co

p-Adic Models of Ultrametric Diffusion Constrained by Hierarchical Energy Landscapes

We demonstrate that p-adic analysis is a natural basis for the construction of a wide variety of the ultrametric diffusion models constrained by hierarchical energy landscapes. A general analytical description in terms of p-adic analysis is given for a class of models. Two exactly solvable examples, i.e. the ultrametric diffusion constraned by the linear energy landscape and the ultrametric diffusion with reaction sink, are considered. We show that such models can be applied to both the relaxation in complex systems and the rate processes coupled to rearrangenment of the complex surrounding.Comment: 14 pages, 6 eps figures, LaTeX 2.0

Quelques plats pour la m\'etrique de Hofer

We show, by an elementary and explicit construction, that the group of Hamiltonian diffeomorphisms of certain symplectic manifolds, endowed with Hofer's metric, contains subgroups quasi-isometric to Euclidean spaces of arbitrary dimension.Comment: 9 pages, minor change

Anomalous relaxation and self-organization in non-equilibrium processes

We study thermal relaxation in ordered arrays of coupled nonlinear elements with external driving. We find, that our model exhibits dynamic self-organization manifested in a universal stretched-exponential form of relaxation. We identify two types of self-organization, cooperative and anti-cooperative, which lead to fast and slow relaxation, respectively. We give a qualitative explanation for the behavior of the stretched exponent in different parameter ranges. We emphasize that this is a system exhibiting stretched-exponential relaxation without explicit disorder or frustration.Comment: submitted to PR

Structure of Extremely Nanosized and Confined In-O Species in Ordered Porous Materials

Perturbed-angular correlation, x-ray absorption, and small-angle x-ray scattering spectroscopies were suitably combined to elucidate the local structure of highly diluted and dispersed InOx species confined in porous of ZSM5 zeolite. These novel approach allow us to determined the structure of extremely nanosized In-O species exchanged inside the 10-atom-ring channel of the zeolite, and to quantify the amount of In2O3 crystallites deposited onto the external zeolite surface.Comment: 4 pages, 5 postscript figures, REVTEX4, published in Physical Review Letter

p-Adic description of characteristic relaxation in complex systems

This work is a further development of an approach to the description of relaxation processes in complex systems on the basis of the p-adic analysis. We show that three types of relaxation fitted into the Kohlrausch-Williams-Watts law, the power decay law, or the logarithmic decay law, are similar random processes. Inherently, these processes are ultrametric and are described by the p-adic master equation. The physical meaning of this equation is explained in terms of a random walk constrained by a hierarchical energy landscape. We also discuss relations between the relaxation kinetics and the energy landscapes.Comment: AMS-LaTeX (+iopart style), 9 pages, submitted to J.Phys.