218 research outputs found
Dynamical tunneling in molecules: Quantum routes to energy flow
Dynamical tunneling, introduced in the molecular context, is more than two
decades old and refers to phenomena that are classically forbidden but allowed
by quantum mechanics. On the other hand the phenomenon of intramolecular
vibrational energy redistribution (IVR) has occupied a central place in the
field of chemical physics for a much longer period of time. Although the two
phenomena seem to be unrelated several studies indicate that dynamical
tunneling, in terms of its mechanism and timescales, can have important
implications for IVR. Examples include the observation of local mode doublets,
clustering of rotational energy levels, and extremely narrow vibrational
features in high resolution molecular spectra. Both the phenomena are strongly
influenced by the nature of the underlying classical phase space. This work
reviews the current state of understanding of dynamical tunneling from the
phase space perspective and the consequences for intramolecular vibrational
energy flow in polyatomic molecules.Comment: 37 pages and 23 figures (low resolution); Int. Rev. Phys. Chem.
(Review to appear in Oct. 2007
Geometric Mixing, Peristalsis, and the Geometric Phase of the Stomach
Mixing fluid in a container at low Reynolds number - in an inertialess
environment - is not a trivial task. Reciprocating motions merely lead to
cycles of mixing and unmixing, so continuous rotation, as used in many
technological applications, would appear to be necessary. However, there is
another solution: movement of the walls in a cyclical fashion to introduce a
geometric phase. We show using journal-bearing flow as a model that such
geometric mixing is a general tool for using deformable boundaries that return
to the same position to mix fluid at low Reynolds number. We then simulate a
biological example: we show that mixing in the stomach functions because of the
"belly phase": peristaltic movement of the walls in a cyclical fashion
introduces a geometric phase that avoids unmixing.Comment: Revised, published versio
The role of chaotic resonances in the solar system
Our understanding of the Solar System has been revolutionized over the past
decade by the finding that the orbits of the planets are inherently chaotic. In
extreme cases, chaotic motions can change the relative positions of the planets
around stars, and even eject a planet from a system. Moreover, the spin axis of
a planet-Earth's spin axis regulates our seasons-may evolve chaotically, with
adverse effects on the climates of otherwise biologically interesting planets.
Some of the recently discovered extrasolar planetary systems contain multiple
planets, and it is likely that some of these are chaotic as well.Comment: 28 pages, 9 figure
Comparison of Newtonian and Special-Relativistic Trajectories with the General-Relativistic Trajectory for a Low-Speed Weak-Gravity System
We show, contrary to expectation, that the trajectory predicted by general-relativistic mechanics for a low-speed weak-gravity system is not always well-approximated by the trajectories predicted by special-relativistic and Newtonian mechanics for the same parameters and initial conditions. If the system is dissipative, the breakdown of agreement occurs for chaotic trajectories only. If the system is non-dissipative, the breakdown of agreement occurs for chaotic trajectories and non-chaotic trajectories. The agreement breaks down slowly for non-chaotic trajectories but rapidly for chaotic trajectories. When the predictions are different, general-relativistic mechanics must therefore be used, instead of special-relativistic mechanics (Newtonian mechanics), to correctly study the dynamics of a weak-gravity system (a low-speed weak-gravity system)
Violation of the transit-time limit toward generation of ultrashort electron bunches with controlled velocity chirp
Various methods to generate ultrashort electron bunches for the ultrafast science evolved from the simple configuration of two-plate vacuum diodes to advanced technologies such as nanotips or photocathodes excited by femtosecond lasers. In a diode either in vacuum or of solid-state, the transit-time limit originating from finite electron mobility has caused spatiotemporal bunch-collapse in ultrafast regime. Here, we show for the first time that abrupt exclusion of transit-phase is a more fundamental origin of the bunch-collapse than the transit-time limit. We found that by significantly extending the cathode-anode gap distance, thereby violating the transit-time limit, the conventional transit-time-related upper frequency barrier in diodes can be removed. Furthermore, we reveal how to control the velocity chirp of bunches leading to ballistic bunch-compression. Demonstration of 0.707 THz-, 46.4 femtosecond-bunches from a 50 mu m-wide diode in three-dimensional particle-in-cell simulations shows a way toward simple and compact sources of ultrafast electron bunches for diverse ultrafast sciences.ope
Anatomy of quantum chaotic eigenstates
The eigenfunctions of quantized chaotic systems cannot be described by
explicit formulas, even approximate ones. This survey summarizes (selected)
analytical approaches used to describe these eigenstates, in the semiclassical
limit. The levels of description are macroscopic (one wants to understand the
quantum averages of smooth observables), and microscopic (one wants
informations on maxima of eigenfunctions, "scars" of periodic orbits, structure
of the nodal sets and domains, local correlations), and often focusses on
statistical results. Various models of "random wavefunctions" have been
introduced to understand these statistical properties, with usually good
agreement with the numerical data. We also discuss some specific systems (like
arithmetic ones) which depart from these random models.Comment: Corrected typos, added a few references and updated some result
Decoherence, Entanglement and Irreversibility in Quantum Dynamical Systems with Few Degrees of Freedom
This review summarizes and amplifies on recent investigations of coupled
quantum dynamical systems in the short wavelength limit. We formulate and
attempt to answer three fundamental questions: (i) What drives a dynamical
quantum system to behave classically ? (ii) What determines the rate at which
two coupled quantum--mechanical systems become entangled ? (iii) How does
irreversibility occur in quantum systems with few degrees of freedom ? We embed
these three questions in the broader context of the quantum--classical
correspondence, which motivates the use of short--wavelength approximations to
quantum mechanics such as the trajectory-based semiclassical methods and random
matrix theory. Doing so, we propose a novel investigative procedure towards
decoherence and the emergence of classicality out of quantumness in dynamical
systems coupled to external degrees of freedom. We reproduce known results
derived using master equation or Lindblad approaches but also generate novel
ones. In particular we show how local exponential instability also affects the
temporal evolution of quantum chaotic dynamical systems. We extensively rely on
numerical experiments to illustrate our findings and briefly comment on
possible extensions to more complex problems involving environments with interacting dynamical systems, going beyond the uncoupled harmonic
oscillator model of Caldeira and Leggett.Comment: Final version, to appear in Advances in Physic
Biological Process Linkage Networks
BACKGROUND. The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known about interactions between higher order biological systems, such as biological pathways and processes. We propose a methodology for gleaning patterns of interactions between biological processes by analyzing protein-protein interactions, transcriptional co-expression and genetic interactions. At the heart of the methodology are the concept of Linked Processes and the resultant network of biological processes, the Process Linkage Network (PLN). RESULTS. We construct, catalogue, and analyze different types of PLNs derived from different data sources and different species. When applied to the Gene Ontology, many of the resulting links connect processes that are distant from each other in the hierarchy, even though the connection makes eminent sense biologically. Some others, however, carry an element of surprise and may reflect mechanisms that are unique to the organism under investigation. In this aspect our method complements the link structure between processes inherent in the Gene Ontology, which by its very nature is species-independent. As a practical application of the linkage of processes we demonstrate that it can be effectively used in protein function prediction, having the power to increase both the coverage and the accuracy of predictions, when carefully integrated into prediction methods. CONCLUSIONS. Our approach constitutes a promising new direction towards understanding the higher levels of organization of the cell as a system which should help current efforts to re-engineer ontologies and improve our ability to predict which proteins are involved in specific biological processes.Lynn and William Frankel Center for Computer Science; the Paul Ivanier center for robotics research and production; National Science Foundation (ITR-048715); National Human Genome Research Institute (1R33HG002850-01A1, R01 HG003367-01A1); National Institute of Health (U54 LM008748
Josephson Junctions and AdS/CFT Networks
We propose a new holographic model of Josephson junctions (and networks
thereof) based on designer multi-gravity, namely multi-(super)gravity theories
on products of distinct asymptotically AdS spacetimes coupled by mixed boundary
conditions. We present a simple model of a Josephson junction (JJ) that
exhibits the well-known current-phase sine relation of JJs. In one-dimensional
chains of holographic superconductors we find that the Cooper-pair condensates
are described by a discretized Schrodinger-type equation. Such non-integrable
equations, which have been studied extensively in the past in condensed matter
and optics applications, are known to exhibit complex behavior that includes
periodic and quasiperiodic solutions, chaotic dynamics, soliton and kink
solutions. In our setup these solutions translate to holographic configurations
of strongly-coupled superconductors in networks with weak site-to-site
interactions that exhibit interesting patterns of modulated superconductivity.
In a continuum limit our equations reduce to generalizations of the
Gross-Pitaevskii equation. We comment on the many possible extensions and
applications of this new approach.Comment: 39 pages, 11 figures; v2 clarified the nature and computation of the
Josephson current in subsec. 3.2 and specific properties of the two-site
system, analogous minor modifications in subsec. 4.4 and added a new subsec.
4.5 with a new fig.
Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
Summary
Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (TP53, ATRX, RB1) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types
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