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Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…

Biomolecules · Quantitative Biology 2016-11-17 T. Andrew Binkowski , Bhaskar DasGupta , Jie Liang

We study the translational motions of homonuclear diatomic molecules prepared in their ${}^3\Sigma$ electronic states, deeply bound vibrational states, and rotational states of well-defined parity. The trapping potential arises due to the…

Mathematical Physics · Physics 2026-03-05 Yurij Yaremko , Maria Przybylska , Andrzej J. Maciejewski

Starting with a post-Newtonian description of compact binary systems, we derive a set of equations that describes the evolution of the orbital angular momentum and both spin vectors during inspiral. We find regions of phase space that…

Astrophysics · Physics 2009-11-10 Jeremy D. Schnittman

Non-relativistic conformally invariant systems in a rotating cosmic string (conical) spacetime are analyzed at the classical and quantum levels by means of the gravitoelectromagnetic interpretation of the background. Solutions of the…

High Energy Physics - Theory · Physics 2022-02-02 Luis Inzunza , Mikhail S. Plyushchay

We analyze relativistic corrections to the wave-packet dynamics of the quantum harmonic oscillator within a perturbative framework. General expressions are derived for the leading-order relativistic contributions to the wave-packet…

Quantum Physics · Physics 2026-03-10 Jian Carlo Ramos , Sujoy K. Modak

We discuss a geometrical method to define a preferred reference frame for precessing binary systems and the gravitational waves they emit. This minimal-rotation frame is aligned with the angular-momentum axis and fixes the rotation about…

General Relativity and Quantum Cosmology · Physics 2012-02-02 Michael Boyle , Robert Owen , Harald P. Pfeiffer

The behavior of coupled harmonic oscillators in systems with specified boundary conditions is typically characterized by resonances whose frequency spectra represent harmonics according to properties of the individual oscillators, the…

Classical Physics · Physics 2009-11-13 Douglas J. Ballon , Henning U. Voss

Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…

Molecular Networks · Quantitative Biology 2009-11-13 Simone Pigolotti , Sandeep Krishna , Mogens H. Jensen

We present an analytic model specifically designed to address the long standing issue of small scale structure on cosmic string networks. The model is derived from the microscopic string equations, together with a few motivated assumptions.…

General Relativity and Quantum Cosmology · Physics 2008-12-23 Jorge V. Rocha

We identify that both the dynamic core polarization and dynamic orbital deformation are important in the orientation-dependent high-harmonic generation of CO molecules subjected to intense few cycle laser fields. These polarization dynamics…

Atomic Physics · Physics 2015-06-19 Bin Zhang , Jianmin Yuan , Zengxiu Zhao

The influence of the orbital symmetry on the ellipticity of the high-order harmonics is investigated. It is found that the ellipticity maps have distinct shapes for the molecular orbital with different symmetry. Our analysis shows that the…

Optics · Physics 2013-12-30 Meiyan Qin , Xiaosong Zhu , Kunlong Liu , Qingbin Zhang , Peixiang Lu

We introduce a method for accurate quantum chemical calculations based on a simple variational wave function, defined by a single geminal that couples all the electrons into singlet pairs, combined with a real space correlation factor. The…

Materials Science · Physics 2009-10-22 M. Marchi , S. Azadi , M. Casula , S. Sorella

We consider high-frequency local vibrations anharmonically coupled with low-frequency modes in a planar lattice of adsorbed molecules. The effect of lateral intermolecular interactions on the spectral line shape for local vibrations is…

Condensed Matter · Physics 2007-05-23 I. V. Kuzmenko , V. M. Rozenbaum

The evolution of occupied volume under progressive fragmentation of granular matter is studied using a purely geometric model. Rather than modelling disorder directly, properties are investigated by analysing highly ordered reference…

Soft Condensed Matter · Physics 2026-03-25 Malkhazi A. Meladze

In the framework of simple spin-boson Hamiltonian we study an interplay between dynamic and spectral roots to stochastic-like behavior. The Hamiltonian describes an initial vibrational state coupled to discrete dense spectrum reservoir. The…

Mesoscale and Nanoscale Physics · Physics 2015-05-19 V. A. Benderskii , E. I. Kats

Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the…

Other Condensed Matter · Physics 2015-12-15 M. Apostol , L. C. Cune

We present the experimental and theoretical details of our recent published letter [Phys. Rev. Lett. 115. 123002] on synchronized high-harmonic and terahertz-wave spectroscopy (HATS) from nonadiabatically aligned nitrogen molecules in…

Atomic Physics · Physics 2016-06-03 Yindong Huang , Chao Meng , Jing Zhao , Xiaowei Wang , Zhihui Lü , Dongwen Zhang , Jianmin Yuan , Zengxiu Zhao

The rich information content of measurements in the molecular frame rather than the laboratory frame has motivated the development of several methods for aligning gas phase molecules in space. Even so, for asymmetric tops the problem of…

Atomic Physics · Physics 2016-11-23 Varun Makhija , Xiaoming Ren , Drue Gockel , Anh-Thu Le , Vinod Kumarappan

A theoretical study of the rotational dynamics of a linear polar molecule in a two-color non-resonant cw laser field is presented. By systematically considering the interactions of this field with the electric dipole moment, polarizability…

Quantum Physics · Physics 2020-08-26 David Mellado-Alcedo , Niurka R. Quintero , Rosario González-Férez

In this paper we demonstrate how asymmetric molecular rotational spectra may be introduced to students both "pictorially" and with simple formulae. It is shown that the interpretation of such spectra relies heavily upon pattern recognition.…

Physics Education · Physics 2012-04-17 S. A. Cooke , P. Ohring