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To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…

Biomolecules · Quantitative Biology 2010-07-27 Yonatan Savir , Tsvi Tlusty

Molecular structure elucidation is a fundamental step in understanding chemical phenomena, with applications in identifying molecules in natural products, lab syntheses, forensic samples, and the interstellar medium. We consider the task of…

Machine Learning · Computer Science 2025-03-04 Austin Cheng , Alston Lo , Kin Long Kelvin Lee , Santiago Miret , Alán Aspuru-Guzik

We suggest an approach to detect the conformation of single molecule by using the photon counting statistics. The generalized Smoluchoswki equation is employed to describe the dynamical process of conformational change of single molecule.…

Chemical Physics · Physics 2014-11-13 Yonggang Peng , Zhen-Dong Sun , Chuanlu Yang , Yujun Zheng

Two-dimensional electronic spectroscopy provides information on coupling and energy transfer between excited states on ultrafast timescales. Only recently, incoherent fluorescence detection has made it possible to combine this method with…

Optics · Physics 2025-05-14 Sanchayeeta Jana , Simon Durst , Lucas Ludwig , Markus Lippitz

The 'l-Doubling' phenomenon emanates from the coupling between molecular rotations and perpendicular vibrations (bending modes) in polyatomic molecules. This elusive phenomenon has been largely discarded in laser-induced molecular…

Chemical Physics · Physics 2024-10-10 Kfir Rutman Moshe , Dina Rosenberg , Inbar Sternbach , Sharly Fleischer

We use state- and time-resolved coherent Raman spectroscopy to study the rotational dynamics of oxygen molecules in ultra-high rotational states. While it is possible to reach rotational quantum numbers up to $N \approx 50$ by increasing…

Chemical Physics · Physics 2015-06-19 Alexander A. Milner , Aleksey Korobenko , Valery Milner

We propose an approach to probe coherent spin-state dynamics of molecules using circularly polarized hard x-ray pulses. For the dynamically aligned nitric oxide molecules in a coherent superposition spin-orbit coupled electronic state that…

Optics · Physics 2024-01-02 Xiaoyu Mi , Ming Zhang , Zheng Li

We report on a segregation scheme for granular binary mixtures, where the segregation is performed by a ratchet mechanism realized by a vertically shaken asymmetric sawtooth-shaped base in a quasi-two-dimensional box. We have studied this…

Statistical Mechanics · Physics 2009-11-07 Zeno Farkas , Ferenc Szalai , Dietrich E. Wolf , Tamas Vicsek

Molecular ions can be held in a chain of laser-cooled atomic ions by sympathetic cooling. This system is ideal for performing high-precision molecular spectroscopy with applications in astrochemistry and fundamental physics. Here we show…

Atomic Physics · Physics 2015-08-20 Ncamiso B. Khanyile , Gang Shu , Kenneth R. Brown

Finding the common structural features of two molecules is a fundamental task in cheminformatics. Most drugs are small molecules, which can naturally be interpreted as graphs. Hence, the task is formalized as maximum common subgraph…

Data Structures and Algorithms · Computer Science 2016-10-28 Andre Droschinsky , Nils Kriege , Petra Mutzel

High harmonic generation in the interaction of femtosecond lasers with atoms and molecules opens the path to molecular orbital tomography and to probe the electronic dynamics with attosecond-{\AA}ngstr\"{o}m resolutions. Molecular orbital…

We discuss a method for tracking individual molecules which globally optimizes the likelihood of the connections between molecule positions fast and with high reliability even for high spot densities and blinking molecules. Our method works…

Computer Vision and Pattern Recognition · Computer Science 2013-04-01 Andreas Karrenbauer , Dominik Wöll

A new and efficient method for orientation echo spectroscopy is presented and realized experimentally. The excitation scheme utilizes concerted rotational excitations by both ultrashort terahertz and near-IR pulses and its all-optical…

Chemical Physics · Physics 2022-12-07 Ran Damari , Amit Beer , Sharly Fleischer

Symmetry is a key feature observed in nature (from flowers and leaves, to butterflies and birds) and in human-made objects (from paintings and sculptures, to manufactured objects and architectural design). Rotational, translational, and…

Computer Vision and Pattern Recognition · Computer Science 2019-08-28 Felice De Luca , Md Iqbal Hossain , Stephen Kobourov

Making use of a droplet-epitaxial technique, we realize nanometer-sized quantum ring complexes, consisting of a well-defined inner ring and an outer ring. Electronic structure inherent in the unique quantum system is analyzed using a…

Materials Science · Physics 2009-11-11 T. Kuroda , T. Mano , T. Ochiai , S. Sanguinetti , K. Sakoda , G. Kido , N. Koguchi

A two level model of a single molecule undergoing spectral diffusion dynamics and interacting with a sequence of two short laser pulses is investigated. Analytical solution for the probability of n=0,1,2 photon emission events for the…

Chemical Physics · Physics 2009-11-13 F. Shikerman , E. Barkai

The vibrational behavior of molecules serves as a crucial fingerprint of their structure, chemical state, and surrounding environment. Neutron vibrational spectroscopy provides comprehensive measurements of vibrational modes without…

Chemical Physics · Physics 2025-02-19 Bowen Han , Pei Zhang , Kshitij Mehta , Massimiliano Lupo Pasini , Mingda Li , Yongqiang Cheng

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a…

Machine Learning · Computer Science 2023-01-30 Michael Murphy , Stefanie Jegelka , Ernest Fraenkel , Tobias Kind , David Healey , Thomas Butler

We report the rotationally resolved spectrum of a single polyatomic molecular ion in the gas phase. Building upon the recently developed inelastic recoil spectroscopy (IRS) technique, we have achieved a spectral resolution sufficient to…

Using a spectrum obtained under moderate (of order 1 arcsecond) seeing, we show that the double nucleus in M31 produces a strong kinematic signature even though the individual components are not spatially resolved. The signature consists of…

Astrophysics · Physics 2016-06-08 J. Gerssen , K. Kuijken , M. R. Merrifield