Spectral analysis of electron transfer kinetics II

Electron transfer processes in Debye solvents are studied using a spectral analysis method recently proposed. Spectral structure of a nonadiabatic two-state diffusion equation is investigated to reveal various kinetic regimes characterized by a broad range of physical parameters; electronic coupling, energy bias, reorganization energy, and solvent relaxation rate. Within this unified framework, several kinetic behaviors of the electron transfer kinetics, including adiabatic Rabi oscillation, crossover from the nonadiabatic to adiabatic limits, transition from the incoherent to coherent kinetic limits, and dynamic bath effect, are demonstrated and compared with results from previous theoretical models. Dynamics of the electron transfer system is also calculated with the spectral analysis method. It is pointed out that in the large reorganization energy case the nonadiabatic diffusion equation exhibits a non-physical behavior, yielding a negative eigenvalue.Comment: submitted for a publication in Journal of Chemical Physic

Three-loop HTL gluon thermodynamics at intermediate coupling

We calculate the thermodynamic functions of pure-glue QCD to three-loop order using the hard-thermal-loop perturbation theory (HTLpt) reorganization of finite temperature quantum field theory. We show that at three-loop order hard-thermal-loop perturbation theory is compatible with lattice results for the pressure, energy density, and entropy down to temperatures $T\simeq3\;T_c$. Our results suggest that HTLpt provides a systematic framework that can used to calculate static and dynamic quantities for temperatures relevant at LHC.Comment: 24 pages, 13 figs. 2nd version: improved discussion and fixing typos. Published in JHE

Game Theoretic Analysis of Negotiations under Bankruptcy

We extend the contingent claims framework for the levered firm in explicitly modeling the resolution of financial distress under formal bankruptcy as a non-cooperative game between claimants under the supervision of the bankruptcy judge. The identity of the class of claimants proposing the first reorganization plan is found to be a key determinant of the likelihood of liquidation and of the renegotiated value of claims. Our quantitative results confirm the economic intuition that a bankruptcy design must trade-off the initial priority of claims with the viability of reorganized firms.Bankruptcy procedure, game theory, dynamic programming

Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors.

Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7) bound to its ligand CCL21

Organization of Multi-Agent Systems: An Overview

In complex, open, and heterogeneous environments, agents must be able to reorganize towards the most appropriate organizations to adapt unpredictable environment changes within Multi-Agent Systems (MAS). Types of reorganization can be seen from two different levels. The individual agents level (micro-level) in which an agent changes its behaviors and interactions with other agents to adapt its local environment. And the organizational level (macro-level) in which the whole system changes it structure by adding or removing agents. This chapter is dedicated to overview different aspects of what is called MAS Organization including its motivations, paradigms, models, and techniques adopted for statically or dynamically organizing agents in MAS.Comment: 12 page

Self-Configuring Socio-Technical Systems: Redesign at Runtime

Modern information systems are becoming more and more socio-technical systems, namely systems composed of human (social) agents and software (technical) systems operating together in a common environment. The structure of such systems has to evolve dynamically in response to the changes of the environment. When new requirements are introduced, when an actor leaves the system or when a new actor comes, the socio-technical structure needs to be redesigned and revised. In this paper, an approach to dynamic reconfiguration of a socio-technical system structure in response to internal or external changes is proposed. The approach is based on planning techniques for generating possible alternative configurations, and local strategies for their evaluation. The reconfiguration mechanism is presented, which makes the socio-technical system self-configuring, and the approach is discussed and analyzed on a simple case study

Etiology of phantom limb syndrome: Insights from a 3D default space consciousness model

In this article, we examine phantom limb syndrome to gain insights into how the brain functions as the mind and how consciousness arises. We further explore our previously proposed consciousness model in which consciousness and body schema arise when information from throughout the body is processed by corticothalamic feedback loops and integrated by the thalamus. The parietal lobe spatially maps visual and non-visual information and the thalamus integrates and recreates this processed sensory information within a three-dimensional space termed the ‘‘3D default space.’’ We propose that phantom limb syndrome and phantom limb pain arise when the afferent signaling from the amputated limb is lost but the neural circuits remain intact. In addition, integration of conflicting sensory information within the default 3D space and the loss of inhibitory afferent feedback to efferent motor activity from the amputated limb may underlie phantom limb pain

Functional connectivity in relation to motor performance and recovery after stroke.

Plasticity after stroke has traditionally been studied by observing changes only in the spatial distribution and laterality of focal brain activation during affected limb movement. However, neural reorganization is multifaceted and our understanding may be enhanced by examining dynamics of activity within large-scale networks involved in sensorimotor control of the limbs. Here, we review functional connectivity as a promising means of assessing the consequences of a stroke lesion on the transfer of activity within large-scale neural networks. We first provide a brief overview of techniques used to assess functional connectivity in subjects with stroke. Next, we review task-related and resting-state functional connectivity studies that demonstrate a lesion-induced disruption of neural networks, the relationship of the extent of this disruption with motor performance, and the potential for network reorganization in the presence of a stroke lesion. We conclude with suggestions for future research and theories that may enhance the interpretation of changing functional connectivity. Overall findings suggest that a network level assessment provides a useful framework to examine brain reorganization and to potentially better predict behavioral outcomes following stroke