date
timestamp[s]
title
stringlengths
6
286
authors
stringlengths
5
4.88k
abstract
stringlengths
24
3.38k
journal
stringlengths
0
267
doi
stringlengths
12
64
2014-12-12T00:00:00
Contribution of resonance tunneling of molecule to physical observables
P. M. Krassovitskiy, F. M. Pen'kov
Probabilities of resonant tunneling through a potential barrier are compared for a rigid molecule and an excited molecule. It is shown that the resonance spectrum is mainly governed by the transmission resonance spectrum of the rigid molecule. Analytical expressions for the probability for the tunneling of the rigid mo...
Journal of Physics B: Atomic, Molecular and Optical Physics, Volume 47, Number 22, 28 November 2014, pp. 225210-225214(5)
10.1088/0953-4075/47/22/225210
2018-03-20T00:00:00
Classical and quantum rotation numbers of asymmetric top molecules
K. Hamraoui, L. Van Damme, P. Mardesic, D. Sugny
We study the classical and quantum rotation numbers of the free rotation of asymmetric top molecules. We show numerically that the quantum rotation number converges to its classical analog in the semi-classical limit. Different asymmetric molecules such as the water molecule are taken as illustrative example. A simple ...
Physical Review A 97, 032118 (2018)
10.1103/PhysRevA.97.032118
2020-04-17T00:00:00
Continuous Representation of Molecules Using Graph Variational Autoencoder
Mohammadamin Tavakoli, Pierre Baldi
In order to continuously represent molecules, we propose a generative model in the form of a VAE which is operating on the 2D-graph structure of molecules. A side predictor is employed to prune the latent space and help the decoder in generating meaningful adjacency tensor of molecules. Other than the potential applica...
null
2020-07-07T00:00:00
Photodissociation of long-range Rydberg molecules
Michael Peper, Johannes Deiglmayr
We present photodissociation of ultracold long-range Rydberg molecules as a tool to characterize their electronic properties. We photoassociate K2 37P molecules with highly entangled electronic and nuclear spins of the two bound atoms and quantify the entanglement by projection of the molecular state onto non-interacti...
Phys. Rev. A 102, 062819 (2020)
10.1103/PhysRevA.102.062819
2020-07-16T00:00:00
Fragmentation of molecules by virtual photons from remote neighbors
Lorenz S. Cederbaum
It is shown that a molecule can dissociate by the energy transferred from a remote neighbor. This neighbor can be an excited neutral or ionic atom or molecule. If it is an atom, the transferred energy is, of course, electronic and in the case of molecules it can also be vibrational. Explicit examples are given which de...
null
2020-08-07T00:00:00
Effective discrimination of chiral molecules in a cavity
Yi-Hao Kang, Zhi-Cheng Shi, Jie Song, Yan Xia
We present a scheme to realize precise discrimination of chiral molecules in a cavity. Assisted by additional laser pulses, cavity fields can evolve to different coherence states with contrary-sign displacements according to the handedness of molecules. Consequently, the handedness of molecules can be read out with hom...
null
2020-11-05T00:00:00
Transformer Based Molecule Encoding for Property Prediction
Prateeth Nayak, Andrew Silberfarb, Ran Chen, Tulay Muezzinoglu, John Byrnes
Neural methods of molecule property prediction require efficient encoding of structure and property relationship to be accurate. Recent work using graph algorithms shows limited generalization in the latent molecule encoding space. We build a Transformer-based molecule encoder and property predictor network with novel ...
null
2020-12-18T00:00:00
A general approach to state-dependent optical tweezer traps for polar molecules
L. Caldwell, M. R. Tarbutt
State-dependent optical tweezers can be used to trap a pair of molecules with a separation much smaller than the wavelength of the trapping light, greatly enhancing the dipole-dipole interaction between them. Here we describe a general approach to producing these state-dependent potentials using the tensor part of the ...
Phys. Rev. Research 3, 013291 (2021)
10.1103/PhysRevResearch.3.013291
2021-03-01T00:00:00
Laser cooled molecules
N. J. Fitch, M. R. Tarbutt
The last few years have seen rapid progress in the application of laser cooling to molecules. In this review, we examine what kinds of molecules can be laser cooled, how to design a suitable cooling scheme, and how the cooling can be understood and modelled. We review recent work on laser slowing, magneto-optical trapp...
Adv. At. Mol. Opt. Phys. 70, 157-262 (2021)
10.1016/bs.aamop.2021.04.003
2021-05-18T00:00:00
Collective Effects of Organic Molecules based on Holstein-Tavis-Cummings Model
Quansheng Zhang, Ke Zhang
We study the collective effects of an ensemble of organic molecules confined in an optical cavity based on Holstein-Tavis-Cummings model. By using the quantum Langevin approach and adiabatically eliminating the degree of freedom of the vibrational motion, we analytically obtain the expression of the cavity transmission...
10.1088/1361-6455/ac0afa
2021-12-10T00:00:00
Identical particles exchange symmetry and the electric dipole moment in molecules
Guglielmo M. Tino
Based on fundamental symmetries, molecules cannot have a permanent electric dipole moment although it is commonly used in the literature to explain the different molecular spectra for heteronuclear and homonuclear molecules. Electric-dipole rotational and vibrational spectra can indeed be observed in heteronuclear mole...
Published in: Symmetry 14(11), 2397 (2022)
10.3390/sym14112397
2022-02-14T00:00:00
Disentangle VAE for Molecular Generation
Yanbo Wang, Qianqian Song
Automatic molecule generation plays an important role on drug discovery and has received a great deal of attention in recent years thanks to deep learning successful use. Graph-based neural network represents state of the art methods on automatic molecule generation. However, it is still challenging to generate molecul...
null
2022-03-17T00:00:00
MolecuSense: Using Force-Feedback Gloves for Creating and Interacting with Ball-and-Stick Molecules in VR
Patrick Gebhardt, Xingyao Yu, Andreas Köhn, Michael Sedlmair
We contribute MolecuSense, a virtual version of a physical molecule construction kit, based on visualization in Virtual Reality (VR) and interaction with force-feedback gloves. Targeting at chemistry education, our goal is to make virtual molecule structures more tangible. Results of an initial user study indicate that...
10.1145/3554944.3554956
2022-05-10T00:00:00
FlavorDB2: An Updated Database of Flavor Molecules
Nishant Grover, Mansi Goel, Devansh Batra, Neelansh Garg, Rudraksh Tuwani, Apuroop Sethupathy, Ganesh Bagler
Flavor is expressed through interaction of molecules via gustatory and olfactory mechanisms. Knowing the utility of flavor molecules in food and fragrances, it is valuable to add a comprehensive repository of flavor compounds characterizing their flavor profile, chemical properties, regulatory status, consumption stati...
null
2022-06-28T00:00:00
First passage time for $g$--subdiffusion process of vanishing particles
Tadeusz Kosztołowicz
Subdiffusion equation and molecule survival equation, both with Caputo fractional time derivatives with respect to another functions $g_1$ and $g_2$, respectively, are used to describe diffusion of a molecule that can disappear at any time with a constant probability. The process can be interpreted as ``ordinary'' subd...
10.1103/PhysRevE.106.L022104
2023-01-05T00:00:00
Localized nonlinear excitations of a columnar chain of coronene molecules
Alexander V. Savin, Sergey V. Dmitriev
The nonlinear dynamics of a one-dimensional molecular crystal in the form of a chain of planar coronene molecules is analyzed. Using molecular dynamics, it is shown that a chain of coronene molecules supports acoustic solitons, rotobreathers, and discrete breathers. An increase in the size of planar molecules in a chai...
null
2003-02-04T00:00:00
Dynamics of Bound and Free Water in an Aqueous Micellar Solution : Analysis of the Lifetime and Vibrational Frequencies of Hydrogen Bonds at a Complex Interface
Subrata Pal, Sundaram Balasubramanian, Biman Bagchi
In order to understand the nature and dynamics of interfacial water molecules on the surface of complex systems, large scale molecular dynamics simulations of an aqueous micelle of cesium perfluorooctanoate surfactant molecules have been carried out. The lifetime and the intermolecular vibrational frequencies of the hy...
10.1103/PhysRevE.67.061502
2004-08-02T00:00:00
Single molecule Raman spectroscopy and local work function fluctuations
Gilad Haran
Single molecule Raman spectroscopy provides information on individual molecules with vibrational-level resolution. The unique mechanisms leading to the huge Raman cross-section enhancement necessary for single molecule sensitivity are under intense investigation in several laboratories. We recently analyzed large spect...
null
2007-10-31T00:00:00
Molecular formations in ultracold mixtures of interacting and noninteracting atomic gases
T. Nishimura, A. Matsumoto, H. Yabu
Atom-molecule equilibrium for molecular formation processes is discussed for boson-fermion, fermion-fermion, and boson-boson mixtures of ultracold atomic gases in the framework of quasichemical equilibrium theory. After presentation of the general formulation, zero-temperature phase diagrams of the atom-molecule equili...
Phys. Rev. A 77, 063612 (2008)
10.1103/PhysRevA.77.063612
2008-09-04T00:00:00
Understanding the electroluminescence emitted by single molecules in scanning tunneling microscopy experiments
John Buker, George Kirczenow
We explore theoretically the electroluminescence of single molecules. We adopt a local-electrode framework that is appropriate for scanning tunneling microscopy (STM) experiments where electroluminescence originates from individual molecules of moderate size on complex substrates: Couplings between the STM tip and mole...
10.1103/PhysRevB.78.125107
2010-09-21T00:00:00
Positron-molecule interactions: resonant attachment, annihilation, and bound states
G. F. Gribakin, J. A. Young, C. M. Surko
This article presents an overview of current understanding of the interaction of low-energy positrons with molecules with emphasis on resonances, positron attachment and annihilation. Annihilation rates measured as a function of positron energy reveal the presence of vibrational Feshbach resonances (VFR) for many polya...
Reviews of Modern Physics, Volume 82, pages 2557-2607 (2010)
10.1103/RevModPhys.82.2557
2012-01-27T00:00:00
Optical detection of single non-absorbing molecules using the surface plasmon of a gold nanorod
Peter Zijlstra, Pedro M. R. Paulo, Michel Orrit
Current optical detection schemes for single molecules require light absorption, either to produce fluorescence or direct absorption signals. This severely limits the range of molecules that can be detected, because most molecules are purely refractive. Metal nanoparticles or dielectric resonators detect non-absorbing ...
10.1038/nnano.2012.51
2012-08-16T00:00:00
Inelastic Tunneling Spectroscopy of Gold-Thiol and Gold-Thiolate Interfaces in Molecular Junctions: The Role of Hydrogen
Firuz Demir, George Kirczenow
It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen ato...
10.1063/1.4748379
2014-01-15T00:00:00
Monte Carlo Study of a wide range of Molecular Spintronics Devices
Pawan Tyagi, Christopher D Angelo, Collin Baker
Molecular spintronics devices (MSDs) are highly promising candidates for enabling quantum computation and revolutionizing computer logic and memory. An advanced MSD will require the placement of magnetic molecules between the two ferromagnetic (FM) electrodes. Recent experimental studies showed that some magnetic molec...
Nano Vol. 10, No. 04, 1550056 (2015)
10.1142/S1793292015500563
2016-09-20T00:00:00
Systematic Theoretical Study on the Interstellar Carbon Chain Molecules
Emmanuel E. Etim, Prasanta Gorai, Ankan Das, Sandip K. Chakrabarti, Elangannan Arunan
In an effort to further our interest in understanding basic chemistry of interstellar molecules, we carry out here an extensive investigation of the stabilities of interstellar carbon chains; Cn, H2Cn, HCnN and CnX (X=N, O, Si, S, H, P, H-, N-). These sets of molecules accounts for about 20% of all the known interstell...
10.3847/0004-637X/832/2/144
2018-10-14T00:00:00
Astronomical Creation of Cyclic-C3H2 and Chain-C3 Due to Interstellar Deep Photoionization
Norio Ota
Astronomical evolution mechanism of small size polycyclic aromatic hydrocarbon (PAH) was analyzed using the first principles quantum-chemical calculation. Starting model molecule was benzene (C6H6), which would be transformed to (C5H5) due to carbon void created by interstellar high speed proton attack. In a protoplane...
null
2017-03-03T00:00:00
Decay behaviors of Pc hadronic molecules
Yong-hui Lin, Chao-wei Shen, Feng-kun Guo, Bing-song Zou
The $P_c(4380)$ and $P_c(4450)$ states observed recently by LHCb experiment were proposed to be either $\bar{D} \Sigma_c^*$ or $\bar{D}^* \Sigma_c$ S-wave bound states of spin parity $J^P={\frac32}^-$. We analyze the decay behaviors of such two types of hadronic molecules within the effective Lagrangian framework. With...
Phys. Rev. D 95, 114017 (2017)
10.1103/PhysRevD.95.114017
2017-05-25T00:00:00
Atomic-scale structure analysis of a molecule at a (6-nanometer)$^3$ ice crystal
Xi Kong, Fazhan Shi, Zhiping Yang, Pengfei Wang, Nicole Raatz, Jan Meijer, Jiangfeng Du
Water is the most important solvent in nature. It is a crucial issue to study interactions among water molecules. Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful tools to detect magnetic interactions for the structure analysis of a molecule with broad applications. But conventional NMR spectro...
Phys. Rev. B 97, 205438 (2018)
10.1103/PhysRevB.97.205438
2022-03-08T00:00:00
Olfaction-inspired MCs: Molecule Mixture Shift Keying and Cross-Reactive Receptor Arrays
Vahid Jamali, Helene M. Loos, Andrea Buettner, Robert Schober, H. Vincent Poor
In this paper, we propose a novel concept for engineered molecular communication (MC) systems inspired by animal olfaction. We focus on a multi-user scenario where several transmitters wish to communicate with a central receiver. We assume that each transmitter employs a unique mixture of different types of signaling m...
null
2022-09-20T00:00:00
Optical Characterization of a Single Quantum Emitter Based on Vanadium Phthalocyanine Molecules
Richard Escalante, Mohan C. Mathpal, Luis J. Martínez, Loïk Gence, Griselda Garcia, Iván A. González, Jerónimo R. Maze
Single quantum emitters play a fundamental role in the development of quantum technologies such as quantum repeaters, and quantum information processing. Isolating individual molecules with stable optical emission is an essential step for these applications, specially for those molecules that present large coherence ti...
null
2022-10-17T00:00:00
Computational Estimation of the Binding Energies of POx and HPOx (x=2,3) Species
Elettra L. Piacentino, Karin I. Öberg
The distribution of molecules between the gas and solid phase during star and planet formation, determines the trajectory of gas and grain surface chemistry, as well as the delivery of elements to nascent planets. This distribution is primarily set by the binding energies of different molecules to water ice surfaces. W...
10.3847/1538-4357/ac96e2
2022-12-03T00:00:00
Multi-view deep learning based molecule design and structural optimization accelerates the SARS-CoV-2 inhibitor discovery
Chao Pang, Yu Wang, Yi Jiang, Ruheng Wang, Ran Su, Leyi Wei
In this work, we propose MEDICO, a Multi-viEw Deep generative model for molecule generation, structural optimization, and the SARS-CoV-2 Inhibitor disCOvery. To the best of our knowledge, MEDICO is the first-of-this-kind graph generative model that can generate molecular graphs similar to the structure of targeted mole...
null
2023-02-02T00:00:00
Predicting Molecule-Target Interaction by Learning Biomedical Network and Molecule Representations
Jinjiang Guo, Jie Li
The study of molecule-target interaction is quite important for drug discovery in terms of target identification, hit identification, pathway study, drug-drug interaction, etc. Most existing methodologies utilize either biomedical network information or molecule structural features to predict potential interaction link...
null
2000-10-11T00:00:00
A mode-coupling theory for the glassy dynamics of a diatomic probe molecule immersed in a simple liquid
S. -H. Chong, W. Gotze, A. P. Singh
Generalizing the mode-coupling theory for ideal liquid-glass transitions, equations of motion are derived for the correlation functions describing the glassy dynamics of a diatomic probe molecule immersed in a simple glass-forming system. The molecule is described in the interaction-site representation and the equation...
10.1103/PhysRevE.63.011206
2001-09-12T00:00:00
The First Cobalt Single-Molecule Magnet
En-Che Yang, David N Hendrickson, Wolfgang Wernsdorfer, Motohiro Nakano, Roger Sommer, Arnold L Rheingold, Marisol Ledezma-Gairaud, George Christou
The first cobalt molecule to function as a single-molecule magnet, [Co4(hmp)4(MeOH)4Cl4], where hmp- is the anion of hydroxymethylpyridine, is reported. The core of the molecule consists of four Co(II) cations and four hmp- oxygen atoms ions at the corners of a cube. Variable-field and variable-temperature magnetizatio...
10.1063/1.1450813
2003-12-10T00:00:00
Second-order transverse magnetic anisotropy induced by disorders in the single-molecule magnet Mn12
Kyungwha Park, Tunna Baruah, Noam Bernstein, Mark R. Pederson
For the single-molecule magnet Mn12, Cornia et al. recently proposed that solvent molecules may cause the quantum tunneling that requires a lower symmetry than S4. However, magnetic quantum tunneling and electron paramagnetic resonance experiments suggested that the proposed theory may not correspond to the measurement...
10.1103/PhysRevB.69.144426
2003-12-18T00:00:00
End group effect on electrical transport through individual molecules: A microscopic study
Yongqiang Xue, Mark A. Ratner
The effect on molecular transport due to chemical modification of the metal-molecule interface is investigated, using as an example the prototypical molecular device formed by attaching a p-disubstituted benzene molecule onto two gold electrodes through chemically different end groups. Using a first-principles based se...
Phys. Rev. B 69, 85403 (2004)
10.1103/PhysRevB.69.085403
2004-03-19T00:00:00
Atom-molecule equilibration in a degenerate Fermi gas with resonant interactions
J. E. Williams, T. Nikuni, N. Nygaard, C. W. Clark
We present a nonequilibrium kinetic theory describing atom-molecule population dynamics in a two-component Fermi gas with a Feshbach resonance. Key collision integrals emerge that govern the relaxation of the atom-molecule mixture to chemical and thermal equilibrium. Our focus is on the pseudogap regime where molecules...
10.1088/0953-4075/37/21/L01
2006-04-07T00:00:00
Optimal conversion of Bose condensed atoms into molecules via a Feshbach resonance
Jaeyoon Jeong, Chris P. Search, Ivana Djuric
In many experiments involving conversion of quantum degenerate atomic gases into molecular dimers via a Feshbach resonance, an external magnetic field is linearly swept from above the resonance to below resonance. In the adiabatic limit, the fraction of atoms converted into molecules is independent of the functional fo...
10.1103/PhysRevA.74.023619
2006-04-12T00:00:00
Phase Diagram for Self-assembly of Amphiphilic Molecule C12E6 by Dissipative Particle Dynamics Simulation
Hiroaki Nakamura, Yuichi Tamura
In a previous study, dissipative particle dynamics simulation was used to qualitatively clarify the phase diagram of the amphiphilic molecule hexaethylene glycol dodecyl ether (C12E6). In the present study, the hydrophilicity dependence of the phase structure was clarified qualitatively by varying the interaction poten...
Computer Physics Communication, Vol. 169(2005) pp. 139-143
10.1016/j.cpc.2005.03.033
2006-05-08T00:00:00
Preparation of a quantum state with one molecule at each site of an optical lattice
T. Volz, N. Syassen, D. M. Bauer, E. Hansis, S. Dürr, G. Rempe
Ultracold gases in optical lattices are of great interest, because these systems bear a great potential for applications in quantum simulations and quantum information processing, in particular when using particles with a long-range dipole-dipole interaction, such as polar molecules. Here we show the preparation of a q...
Nature Phys. 2, 692 (2006)
10.1038/nphys415
2006-11-21T00:00:00
Can Ballistic Electrons Probe the Electronic Spectra of Individual Buried Molecules?
George Kirczenow
A theoretical study is presented of the ballistic electron emission spectra (BEES) of individual insulating and conducting organic molecules chemisorbed on a silicon substrate and buried under a thin gold film. It is predicted that ballistic electrons injected into the gold film from a scanning tunneling microscope tip...
null
1994-06-02T00:00:00
The Status of Molecules
T. Barnes
This report summarizes the experimental and theoretical status of hadronic molecules, which are weakly-bound states of two or more hadrons. We begin with a brief history of the subject and discuss a few good candidates, and then abstract some signatures for molecules which may be of interest in the classification of po...
null
2003-12-19T00:00:00
Slowing heavy, ground-state molecules using an alternating gradient decelerator
M. R. Tarbutt, H. L. Bethlem, J. J. Hudson, V. L. Ryabov, V. A. Ryzhov, B. E. Sauer, G. Meijer, E. A. Hinds
Cold supersonic beams of molecules can be slowed down using a switched sequence of electrostatic field gradients. The energy to be removed is proportional to the mass of the molecules. Here we report deceleration of YbF, which is 7 times heavier than any molecule previously decelerated. We use an alternating gradient s...
Phys. Rev. Lett. 92, 173002 (2004)
10.1103/PhysRevLett.92.173002
2005-04-21T00:00:00
Molecules Near Absolute Zero and External Field Control of Atomic and Molecular Dynamics
R. V. Krems
This article reviews the current state of the art in the field of cold and ultracold molecules and demonstrates that chemical reactions, inelastic collisions and dissociation of molecules at subKelvin temperatures can be manipulated with external electric or magnetic fields. The creation of ultracold molecules may allo...
10.1080/01442350500167161
2006-11-27T00:00:00
What is the time scale of random sequential adsorption?
Radek Erban, S. Jonathan Chapman
A simple multiscale approach to the diffusion-driven adsorption from a solution to a solid surface is presented. The model combines two important features of the adsorption process: (i) the kinetics of the chemical reaction between adsorbing molecules and the surface; and (ii) geometrical constraints on the surface mad...
10.1103/PhysRevE.75.041116
2006-07-18T00:00:00
A modified approach to the measurement problem: Objective reduction in the retinal molecule prior to conformational change
Fred H. Thaheld
A new analysis of the measurement problem reveals the possibility that collapse of the wavefunction may now take place just before photoisomerization of the rhodopsin molecule in the retinal rods. It is known that when a photon is initially absorbed by the retinal molecule which, along with opsin comprises the rhodopsi...
BioSystems 92 (2008) 114-116
null
2007-05-16T00:00:00
Desorption of hot molecules from photon irradiated interstellar ices
J. D. Thrower, D. J. Burke, M. P. Collings, A. Dawes, P. J. Holtom, F. Jamme, P. Kendall, W. A. Brown, I. P. Clark, H. J. Fraser, M. R. S. McCoustra, N. J. Mason, A. W. Parker
We present experimental measurements of photodesorption from ices of astrophysical relevance. Layers of benzene and water ice were irradiated with a laser tuned to an electronic transition in the benzene molecule. The translational energy of desorbed molecules was measured by time-of-flight (ToF) mass spectrometry. Thr...
10.1086/524097
2008-02-18T00:00:00
Retrieval of interatomic separations of molecules from laser-induced high-order harmonic spectra
Van-Hoang Le, Ngoc-Ty Nguyen, C. Jin, Anh-Thu Le, C. D. Lin
We illustrate an iterative method for retrieving the internuclear separations of N$_2$, O$_2$ and CO$_2$ molecules using the high-order harmonics generated from these molecules by intense infrared laser pulses. We show that accurate results can be retrieved with a small set of harmonics and with one or few alignment an...
J. Phys. B: At. Mol. Opt. Phys. 41, 085603 (2008)
10.1088/0953-4075/41/8/085603
2008-10-10T00:00:00
Coherent Atom-Molecule Oscillations in a Bose-Fermi Mixture
M. L. Olsen, J. D. Perreault, T. D. Cumby, D. S. Jin
We create atom-molecule superpositions in a Bose-Fermi mixture of Rb-87 and K-40 atoms. The superpositions are generated by ramping an applied magnetic field near an interspecies Fano-Feshbach resonance to coherently couple atom and molecule states. Rabi- and Ramsey-type experiments show oscillations in the molecule po...
Phys. Rev. A 80, 030701(R) (2009)
10.1103/PhysRevA.80.030701
2008-12-30T00:00:00
Deeply bound ultracold molecules in an optical lattice
Johann G. Danzl, Manfred J. Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, Andreas Liem, Holger Zellmer, Hanns-Christoph Naegerl
We demonstrate efficient transfer of ultracold molecules into a deeply bound rovibrational level of the singlet ground state potential in the presence of an optical lattice. The overall molecule creation efficiency is 25%, and the transfer efficiency to the rovibrational level |v=73,J=2> is above 80%. We find that the ...
10.1088/1367-2630/11/5/055036
2009-02-13T00:00:00
Hydrogen Storage by Polylithiated Molecules and Nanostructures
Süleyman Er, Gilles A. de Wijs, Geert Brocks
We study polylithiated molecules as building blocks for hydrogen storage materials, using first-principles calculations. $\clifour$ and $\olitwo$ bind 12 and 10 hydrogen molecules, respectively, with an average binding energy of 0.10 and 0.13 eV, leading to gravimetric densities of 37.8 and 40.3 weight % H. Bonding bet...
J. Phys. Chem. C 113, 8997-9002 (2009)
10.1021/jp901305h
2009-09-26T00:00:00
Manifestation of the strong quadrupole light-molecule interaction in the SEHR spectra of symmetrical molecules
A. M. Polubotko
The paper demonstrates possibility of giant enhancement of Surface Enhanced Hyper Raman Scattering on the base of qualitative consideration of electromagnetic field near some models of rough metal surfaces and of some features of the dipole and quadrupole light-molecule interaction, such as it was made in the dipole-qu...
null
2010-09-22T00:00:00
Tuneable molecular doping of corrugated graphene
D. W. Boukhvalov
Density functional theory (DFT) modeling of the physisorption of four different types of molecules (toluene, bromine dimmer, water and nitrogen dioxide) over and above graphene ripples has been performed. For all types of molecules changes of charge transfer and binding energies in respect to flat graphene is found. Th...
Surface Science 604:2190-2193 (2010)
10.1016/j.susc.2010.09.013
2010-12-06T00:00:00
Driving rotational transitions in molecules on a chip
Gabriele Santambrogio, Samuel A. Meek, Mark J. Abel, Liam M. Duffy, Gerard Meijer
Polar molecules in selected quantum states can be guided, decelerated, and trapped using electric fields created by microstructured electrodes on a chip. Here we explore how transitions between two of these quantum states can be induced while the molecules are on the chip. We use CO (a 3-Pi(1), v=0) molecules, prepared...
ChemPhysChem 12 (10), 1799 (2011)
10.1002/cphc.201001007
2011-01-21T00:00:00
Multiple spin state analysis of magnetic nano graphene
Norio Ota, Narjes Gorjizadeh, Yoshiyuki Kawazoe
Recent experiments indicate room-temperature ferromagnetism in graphite-like materials. This paper offers multiple spin state analysis applied to asymmetric graphene molecule to find out mechanism of ferromagnetic nature. First principle density functional theory is applied to calculate spin density, energy and atom po...
null
2011-10-20T00:00:00
Long-lived dipolar molecules and Feshbach molecules in a 3D optical lattice
Amodsen Chotia, Brian Neyenhuis, Steven A. Moses, Bo Yan, Jacob P. Covey, Michael Foss-Feig, Ana Maria Rey, Deborah S. Jin, Jun Ye
We have realized long-lived ground-state polar molecules in a 3D optical lattice, with a lifetime of up to 25 s, which is limited only by off-resonant scattering of the trapping light. Starting from a 2D optical lattice, we observe that the lifetime increases dramatically as a small lattice potential is added along the...
Phys. Rev. Lett. 108, 080405 (2012)
10.1103/PhysRevLett.108.080405
2012-06-18T00:00:00
Noise and Transport Characterization of Single Molecular Break Junctions with Individual Molecule
V. A. Sydoruk, D. Xiang, S. A. Vitusevich, M. V. Petrychuk, A. Vladyka, Y. Zhang, A. Offenhäusser, V. A. Kochelap, A. E. Belyaev, D. Mayer
We studied the noise spectra of molecule-free and molecule-containing mechanically controllable break junctions. Both types of junctions revealed typical 1/ f noise characteristics at different distances between the contacts with square dependence of current noise power spectral density on current. Additional Lorentzia...
J. Appl. Phys. 112, 014908 (2012)
10.1063/1.4736558
2014-03-04T00:00:00
Voltage tuning of vibrational mode energies in single-molecule junctions
Y. Li, P. Doak, L. Kronik, J. B. Neaton, D. Natelson
Vibrational modes of molecules are fundamental properties determined by intramolecular bonding, atomic masses, and molecular geometry, and often serve as important channels for dissipation in nanoscale processes. Although single-molecule junctions have been employed to manipulate electronic structure and related functi...
Proc. Nat. Acad. US 111, 1282-1287 (2014)
10.1073/pnas.1320210111
2014-07-07T00:00:00
Higher-order nonclassical properties of atom-molecule Bose-Einstein Condensate
Sandip Kumar Giri, Kishore Thapliyal, Biswajit Sen, Anirban Pathak
The transient quantum statistical properties of the atoms and molecules in an atom-molecule BEC system are investigated by obtaining a third-order perturbative solution of the Heisenberg's equations of motion corresponding to the Hamiltonian of an atom-molecule BEC system where two atoms can collide to form a molecule....
null
2014-08-21T00:00:00
Cooling and trapping of atoms and molecules by the counter-propagating pulses trains
V. I. Romanenko, Ye. G. Udovitskaya, A. V. Romanenko, L. P. Yatsenko
We discuss a possible one-dimensional trapping and cooling of atoms and molecules due to their non-resonant interaction with the counter-propagating light pulses trains. The counter-propagating pulses form a one-dimensional trap for atoms and molecules, and properly chosen the carrier frequency detuning from the transi...
Phys. Rev. A 90, 053421 (2014)
10.1103/PhysRevA.90.053421
2014-09-25T00:00:00
First-principles Study of the Interactions of Electron Donor and Acceptor Molecules with Phosphorene
Ruiqi Zhang, Bin Li, Jinlong Yang
Density functional theory calculations have been carried out to investigate single-layer phosphorene functionalized with two kinds of organic molecules, i.e. an electrophilic molecule tetracyano-p-quinodimethane (TCNQ) as electron acceptor and a nucleophilic molecule tetrathia-fulvalene (TTF) as electron donor. The TCN...
null
2015-02-23T00:00:00
Calculation of molecular free energies in classical potentials
Asaf Farhi
Free energies of molecules can be calculated by quantum computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free...
10.1088/1367-2630/18/2/023039
2015-04-12T00:00:00
Unwinding of circular helicoidal molecules versus size
Marco Zoli
The thermodynamical stability of a set of circular double helical molecules is analyzed by path integral techniques. The minicircles differ only in \textit{i)} the radius and \textit{ii)} the number of base pairs ($N$) arranged along the molecule axis. Instead, the rise distance is kept constant. For any molecule size,...
Europhys. Lett. 110, 18001 (2015)
10.1209/0295-5075/110/18001
2015-04-24T00:00:00
Kinetics of self-assembly via facilitated diffusion: formation of the transcription complex
Ziya Kalay
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in three-dimensions and one-dimension. Our study is motivated by single molecule level obser...
Phys. Rev. E 92, 042716 (2015)
10.1103/PhysRevE.92.042716
2015-05-13T00:00:00
Theory of long-range ultracold atom-molecule photoassociation
Jesús Pérez-Ríos, Maxence Lepers, Olivier Dulieu
The creation of ultracold molecules is currently limited to diatomic species. In this letter we present a theoretical description of the photoassociation of ultracold atoms and molecules to create ultracold excited triatomic molecules, thus being a novel example of light-assisted ultracold chemical reaction. The calcul...
10.1103/PhysRevLett.115.073201
2015-06-17T00:00:00
Modeling astronomically observed interstellar infrared spectra by ionized carbon pentagon-hexagon molecules (c9h7) n+
Norio Ota
Modeling a promising carrier of the astronomically observed polycyclic aromatic hydrocarbon (PAH), infrared (IR) spectra of ionized molecules (C9H7) n+ were calculated based on density functional theory (DFT). In a previous study, it was found that void induced coronene C23H12++ could reproduce observed spectra from 3 ...
null
2015-09-03T00:00:00
Magic ratios for connectivity-driven electrical conductance of graphene-like molecules
Yan Geng, Sara Sangtarash, Cancan Huang, Hatef Sadeghi, Yongchun Fu, Wenjing Hong, Thomas Wandlowski, Silvio Decurtins, Colin J. Lambert, Shi-Xia Liu
Experiments using a mechanically-controlled break junction and calculations based on density functional theory demonstrate a new magic ratio rule (MRR),which captures the contribution of connectivity to the electrical conductance of graphene-like aromatic molecules. When one electrode is connected to a site i and the o...
Journal of the American Chemical Society, 2015, 137, 4469
10.1021/jacs.5b00335
2015-09-30T00:00:00
Radiation-Induced Correlation between Molecules Nearby Metallic Antenna Array
Yoshiki Osaka, Nobuhiko Yokoshi, Hajime Ishihara
We theoretically investigate optical absorption of molecules embedded nearby metallic antennas by using discrete dipole approximation method. It is found that the spectral peak of the absorption is shifted due to the radiation-induced correlation between the molecules. The most distinguishing feature of our work is to ...
International Journal of Antennas and Propagation, 2015, 747580 (1-6) (2015)
10.1155/2015/747580
2016-02-03T00:00:00
Carbon Chains and Methanol toward Embedded Protostars
Dawn M. Graninger, Olivia H. Wilkins, Karin I. Oberg
Large interstellar organic molecules are potential precursors of prebiotic molecules. Their formation pathways and chemical relationships with one another and simpler molecules are therefore of great interest. In this paper, we address the relationship between two classes of large organic molecules, carbon chains and s...
10.3847/0004-637X/819/2/140
2016-03-01T00:00:00
Two-photon up-conversion affected by inter-molecule correlations near metallic nanostructure
Yoshiki Osaka, Nobuhiko Yokoshi, Hajime Ishihara
We investigate an efficient two-photon up-conversion process in more than one molecule coupled to an optical antenna. In the previous work [Y. Osaka et al., PRL 112, 133601 (2014)], we considered the two-photon up-conversion process in a single molecule within one-dimensional input-output theory, and revealed that cont...
10.1103/PhysRevB.93.155420
2016-04-28T00:00:00
Rydberg atom mediated non-destructive readout of collective rotational states in polar molecule arrays
Elena Kuznetsova, Seth T. Rittenhouse, H. R. Sadeghpour, Susanne F. Yelin
We analyze in detail the possibility to use charge-dipole interaction between a single polar molecule or a 1D molecular array and a single Rydberg atom to read out rotational populations. The change in the Rydberg electron energy is conditioned on the rotational state of the polar molecules, allowing for realization of...
Phys. Rev. A 94, 032325 (2016)
10.1103/PhysRevA.94.032325
2016-10-24T00:00:00
Calculated Structural and Electronic Interactions of the nano dye molecule $\rm Ru(4,\acute{4}-COOH-2,\acute{2}-bpy)_2(NCS)_2$($\rm N3$) with a iodide/triiodide redox shuttle
E. Shomali, I. Abdolhosseini Sarsari, S. Javad Hashemifar, M. Alaei
In this paper, dye sensitized solar cell based on nano dye molecule N3 are investigated by using density functional computations. The main focus is on the N3 dye molecule and corresponding complexes formed at the interface between electrolyte and dye, during the regeneration process. The optimizaed geometry and electro...
Current Applied Physics 17 (2017) 1029e1037
10.1016/j.cap.2017.04.013
2016-10-26T00:00:00
Laser-coolable polyatomic molecules with heavy nuclei
T. A. Isaev, A. V. Zaitsevskii, E. Eliav
Recently a number of diatomic and polyatomics molecules has been identified as a prospective systems for Doppler/Sisyphus cooling. Doppler/Sisyphus cooling allows to decrease the kinetic energy of molecules down to microkelvin temperatures with high efficiency and then capture them to molecular traps, including magneto...
10.1088/1361-6455/aa8f34
2017-02-12T00:00:00
Expectation Values of Some Diatomic Molecules With Quantum Interaction Potential In Schrodinger Equation with Hellmann-Feynman Theorem Via Conventional Nikiforov-Uvarov Method
Ituen B. Okon, Oyebola Popoola, Cecilia N. Isonguyo
In this work, we used a tool of conventional Nikiforov-Uvarov method to determine bound state solution of Schrodinger equation with quantum interaction potential called Hulthen-Yukawa inversely quadratic potential (HYIQP). We obtained the energy eigen values and the total wave function . We employed Hellmann-Feynmann T...
null
2017-04-10T00:00:00
The Symmetry Group Paradox for Non-Rigid Molecules
B. J. Dalton
In many situations the energy levels for a quantum system whose Hamiltonian is invariant under a specific symmetry group are split when the Hamiltonian is replaced by a new one with lower symmetry. In non-rigid molecules quantum tunnelling processes allow the molecule to change between different geometrical configurati...
10.1080/00268976.2017.1347296
2017-06-02T00:00:00
Ultracold Molecule Assembly with Photonic Crystals
J. Pérez-Ríos, May E. Kim, Chen-Lung Hung
Photoassociation (PA) is a powerful technique to synthesize molecules directly and continuously from cold and ultracold atoms into deeply bound molecular states. In freespace, however, PA efficiency is constrained by the number of spontaneous decay channels linking the initial excited molecular state to a sea of final ...
10.1088/1367-2630/aa9b49
2017-07-17T00:00:00
Detecting stimulated-Raman responses of few molecules using Optical Forces
Venkata Ananth Tamma, Lindsey M. Beecher, Jennifer S. Shumaker-Parry, H. Kumar Wickramasinghe
We demonstrate the stimulated Raman near-field microscopy of few molecules, measured only using near-field optical forces thereby eliminating the need for far-field optical detection. The molecules were excited in the near-field without resonant electronic enhancement. We imaged gold nanoparticles of 30 nm diameter fun...
null
2018-05-07T00:00:00
Hybrid atom-molecule quantum walks in one-dimensional optical lattice
Ling Lin, Yongguan Ke, Chunshan He, Chaohong Lee
We study hybrid atom-molecule quantum walks in one-dimensional optical lattices with two interacting bosonic atoms which may be converted into a molecule. The hybrid atom-molecule energy bands include a continuum band and two isolated bands, which respectively correspond to scattering states and dressed bound states (D...
Phys. Rev. A 98, 043628 (2018)
10.1103/PhysRevA.98.043628
2014-02-20T00:00:00
Seeing the vibrational breathing of a single molecule through time-resolved coherent anti-Stokes Raman scattering
Steven Yampolsky, Dmitry A. Fishman, Shirshendu Dey, Eero Hulkko, Mayukh Banik, Eric O. Potma, Vartkess A. Apkarian
The motion of chemical bonds within molecules can be observed in real time, in the form of vibrational wavepackets prepared and interrogated through ultrafast nonlinear spectroscopy. Such nonlinear optical measurements are commonly performed on large ensembles of molecules, and as such, are limited to the extent that e...
null
2014-02-26T00:00:00
Evidence of disorder in biological molecules from single molecule pulling experiments
Changbong Hyeon, Michael Hinczewski, D. Thirumalai
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an exactly solvable model in which the unfolding rate due to mechanical force depends...
Phys. Rev. Lett. (2014) vol. 112, 138101
10.1103/PhysRevLett.112.138101
2015-11-23T00:00:00
Rotational cooling of trapped polyatomic molecules
Rosa Glöckner, Alexander Prehn, Barbara G. U. Englert, Gerhard Rempe, Martin Zeppenfeld
Controlling the internal degrees of freedom is a key challenge for applications of cold and ultracold molecules. Here, we demonstrate rotational-state cooling of trapped methyl fluoride molecules (CH3F) by optically pumping the population of 16 M-sublevels in the rotational states J=3,4,5, and 6 into a single level. By...
Phys. Rev. Lett. 115, 233001 (2015)
10.1103/PhysRevLett.115.233001
2017-10-20T00:00:00
Out-of-plane Enhanced Magnetic Anisotropy Energy in Ni$_{3}$Bz$_{3}$ molecule
Tomás Alonso-Lanza, Jhon W. González, Faustino Aguilera-Granja, Andrés Ayuela
Organometallic complexes formed by transition metals clusters and benzene molecules have already been synthesized, and in selected cases display magnetic properties controlled by external magnetic fields. We have studied Ni$_n$Bz$_n$ complexes made of nickel atoms surrounded by benzene molecules and here we focus speci...
null
2018-06-13T00:00:00
Solvation in the Large Box Limit
Janusz Ginster, Peter Gladbach
In this paper, the authors study the limit of a sharp interface model for the solvation of charged molecules in an implicit solvent as the number of solute molecules and the size of the surrounding box tend to infinity. The energy is given by a combination of local terms accounting for the physical presence of the mole...
null
2018-06-24T00:00:00
Controlling the scattering length of ultracold dipolar molecules
Lucas Lassablière, Goulven Quéméner
By applying a circularly polarized and slightly blue-detuned microwave field with respect to the first excited rotational state of a dipolar molecule, one can engineer a long-range, shallow potential well in the entrance channel of the two colliding partners. As the applied microwave ac-field is increased, the long-ran...
Phys. Rev. Lett. 121, 163402 (2018)
10.1103/PhysRevLett.121.163402
2019-02-01T00:00:00
Impact of Polarity on the Anisotropic Diffusion of Conjugated Organic Molecules on (10-10) Zinc Oxide Surface
Mila Miletic, Karol Palczynski, Matheus Jacobs, Ana Valencia, Caterina Cocchi, Joachim Dzubiella
We study the influence of polarity on the binding and diffusion of single conjugated organic molecules on the inorganic (10-10) zinc oxide surface by means of all-atom molecular dynamics simulations at room temperature and above. In particular, we consider the effects of partial fluorination of the para-sexiphenyl (p-6...
null
2019-02-27T00:00:00
Trilobites, butterflies, and other exotic specimens of long-range Rydberg molecules
Matthew T Eiles
This Ph.D. tutorial discusses ultra-long-range Rydberg molecules, the exotic bound states of a Rydberg atom and one or more ground state atoms immersed in the Rydberg electron's wave function. This novel chemical bond is distinct from an ionic or covalent bond, and is accomplished by a very different mechanism: the Ryd...
10.1088/1361-6455/ab19ca
2011-08-29T00:00:00
Non-local state-swapping of polar molecules in bilayers
A. Pikovski, M. Klawunn, A. Recati, L. Santos
The observation of significant dipolar effects in gases of ultra-cold polar molecules typically demands a strong external electric field to polarize the molecules. We show that even in the absence of a significant polarization, dipolar effects may play a crucial role in the physics of polar molecules in bilayers, provi...
Phys. Rev. A 84, 061605(R) (2011)
10.1103/PhysRevA.84.061605
2016-01-14T00:00:00
Site selection in single-molecule junction for highly reproducible molecular electronics
Satoshi Kaneko, Daigo Murai, Santiago Marqués-González, Hisao Nakamura, Yuki Komoto, Shintaro Fujii, Tomoaki Nishino, Katsuyoshi Ikeda, Kazuhito Tsukagoshi, Manabu Kiguchi
Adsorption sites of molecules critically determine the electric/photonic properties and its stability of heterogeneous molecule-metal interfaces. Then, selectivity of adsorption site is essential for development of the fields including organic electronics, catalysis, and biology. However, due to current technical limit...
null
2018-07-19T00:00:00
Long-lasting field-free alignment of large molecules inside helium nanodroplets
Adam S. Chatterley, Constant Schouder, Lars Christiansen, Benjamin Shepperson, Mette H. Rasmussen, Henrik Stapelfeldt
Molecules with their axes sharply confined in space, available through laser-induced alignment methods, are essential for many current experiments, including ultrafast molecular imaging. Most of these applications require both that the aligning laser field is turned-off, to avoid undesired perturbations, and that the m...
10.1038/s41467-018-07995-0
2018-07-25T00:00:00
Waiting time between charging and discharging processes in molecular junctions
Daniel S. Kosov
When electric current flows through a molecular junction, the molecule constantly charges and discharges by tunnelling electrons. These charging and discharging events occur at specific but random times and separated by stochastic time intervals. These time intervals can be associated with dwelling time for a charge (e...
J Chem Phys. 2018 149(16):164105
10.1063/1.5049770
2012-09-06T00:00:00
Magnetic Feshbach resonances in collisions of non-magnetic closed-shell $^1Σ$ molecules
Alisdair O. G. Wallis, Roman V. Krems
Magnetic Feshbach resonances play a central role in experimental research of atomic gases at ultracold temperatures, as they allow one to control the microscopic interactions between ultracold atoms by tuning an applied magnetic field. These resonances arise due to strong hyperfine interactions between the unpaired ele...
Phys. Rev. A 89, 032716 (2014)
10.1103/PhysRevA.89.032716
2016-07-12T00:00:00
Strongly interacting ultracold polar molecules
Bryce Gadway, Bo Yan
This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole-dipole interactions. Ultracold samples of dipolar molecules with long-range interactions o...
J. Phys. B vol. 49, p. 152002 (2016)
10.1088/0953-4075/49/15/152002
2017-03-21T00:00:00
SMILES Enumeration as Data Augmentation for Neural Network Modeling of Molecules
Esben Jannik Bjerrum
Simplified Molecular Input Line Entry System (SMILES) is a single line text representation of a unique molecule. One molecule can however have multiple SMILES strings, which is a reason that canonical SMILES have been defined, which ensures a one to one correspondence between SMILES string and molecule. Here the fact t...
null
2017-11-16T00:00:00
Posner molecules: From atomic structure to nuclear spins
Michael W. Swift, Chris G. Van de Walle, Matthew P. A. Fisher
We investigate "Posner molecules", calcium phosphate clusters with chemical formula Ca$_9$(PO$_4$)$_6$. Originally identified in hydroxyapatite, Posner molecules have also been observed as free-floating molecules $in$ $vitro$. The formation and aggregation of Posner molecules have important implications for bone growth...
Phys. Chem. Chem. Phys. 20, 12373 (2018)
10.1039/C7CP07720C
2017-12-20T00:00:00
In silico generation of novel, drug-like chemical matter using the LSTM neural network
Peter Ertl, Richard Lewis, Eric Martin, Valery Polyakov
The exploration of novel chemical spaces is one of the most important tasks of cheminformatics when supporting the drug discovery process. Properly designed and trained deep neural networks can provide a viable alternative to brute-force de novo approaches or various other machine-learning techniques for generating nov...
null
2018-09-08T00:00:00
Molecular Hypergraph Grammar with its Application to Molecular Optimization
Hiroshi Kajino
Molecular optimization aims to discover novel molecules with desirable properties. Two fundamental challenges are: (i) it is not trivial to generate valid molecules in a controllable way due to hard chemical constraints such as the valency conditions, and (ii) it is often costly to evaluate a property of a novel molecu...
null
2014-06-10T00:00:00
Fluctuations, correlations and the estimation of concentrations inside cells
Emiliano Pérez Ipiña, Silvina Ponce Dawson
Information transmission in cells occurs quite accurately even when concentration changes are "read" by individual target molecules. In this Letter we study molecule number fluctuations when molecules diffuse and react. We show that, for immobile binding sites, fluctuations in the number of bound molecules are averaged...
null
2014-06-25T00:00:00
Time-reversal symmetry violation in molecules induced by nuclear magnetic quadrupole moments
V. V. Flambaum, D. DeMille, M. G. Kozlov
Recent measurements in paramagnetic molecules improved the limit on the electron electric dipole moment (EDM) by an order of magnitude. Time-reversal (T) and parity (P) symmetry violation in molecules may also come from their nuclei. We point out that nuclear T,P-odd effects are amplified in paramagnetic molecules cont...
Phys. Rev. Lett. 113, 103003 (2014)
10.1103/PhysRevLett.113.103003
2014-06-25T00:00:00
Rotational hybridization, and control of alignment and orientation in triatomic ultralong-range Rydberg molecules
Rosario González-Férez, H. R. Sadeghpour, Peter Schmelcher
We explore the electronic structure and rovibrational properties of an ultralong-range triatomic Rydberg molecule formed by a Rydberg atom and a ground state heteronuclear diatomic molecule. We focus here on interaction of Rb($27s$) Rydberg atom with KRb($N=0$) diatomic polar molecule. There's significant electronic hy...
10.1088/1367-2630/17/1/013021