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2009-01-08T00:00:00 | Mechanically-Controlled Binary Conductance Switching of a Single-Molecule Junction | Su Ying Quek, Maria Kamenetska, Michael L. Steigerwald, Hyoung Joon Choi, Steven G. Louie, Mark S. Hybertsen, J. B. Neaton, L. Venkataraman | Molecular-scale components are expected to be central to nanoscale electronic
devices. While molecular-scale switching has been reported in atomic quantum
point contacts, single-molecule junctions provide the additional flexibility of
tuning the on/off conductance states through molecular design. Thus far,
switching in single-molecule junctions has been attributed to changes in the
conformation or charge state of the molecule. Here, we demonstrate reversible
binary switching in a single-molecule junction by mechanical control of the
metal-molecule contact geometry. We show that 4,4'-bipyridine-gold
single-molecule junctions can be reversibly switched between two conductance
states through repeated junction elongation and compression. Using
first-principles calculations, we attribute the different measured conductance
states to distinct contact geometries at the flexible but stable N-Au bond:
conductance is low when the N-Au bond is perpendicular to the conducting
pi-system, and high otherwise. This switching mechanism, inherent to the
pyridine-gold link, could form the basis of a new class of
mechanically-activated single-molecule switches. | 10.1038/nnano.2009.10 |
|
2009-03-25T00:00:00 | Adsorption of benzene, phenol, propane and carbonic acid molecules on oxidized Al(111) and alpha-Al2O3(0001) surfaces: A first-principles study | Janne Blomqvist, Petri Salo | We present the results of ab initio calculations describing the adsorption of
certain small organic molecules on clean and oxidized Al(111) surfaces as well
as on the alpha-Al2O3(0001) surface. Our results show that adsorption of
benzene on the clean and oxidized Al(111) surfaces is generally weak, the
adsorption energy being at most around -0.5 eV per benzene molecule, and the
molecule adsorbed at a considerable distance from the surfaces. The adsorption
energy varies weakly at the different adsorption sites and as a function of the
oxygen coverage. For the alumina surface, we find no benzene adsorption at all.
We have also calculated a phenol molecule on the aluminium and alumina
surfaces, since it is similar to the benzene molecule. The results show a weak
adsorption for phenol on the alumina surface and no adsorption on the aluminium
or oxidized aluminium surfaces at all. For the propane molecule there is no
adsorption on either the oxidized aluminium or the alumina surface, whereas the
carbonic acid molecule binds strongly to the alumina but not to the aluminium
surface. | J. Phys.: Condens. Matter 21 (2009) 225001 | 10.1088/0953-8984/21/22/225001 |
2009-12-29T00:00:00 | Massively parallel single-molecule manipulation using centrifugal force | Ken Halvorsen, Wesley P. Wong | Precise manipulation of single molecules has already led to remarkable
insights in physics, chemistry, biology and medicine. However, widespread
adoption of single-molecule techniques has been impeded by equipment cost and
the laborious nature of making measurements one molecule at a time. We have
solved these issues with a new approach: massively parallel single-molecule
force measurements using centrifugal force. This approach is realized in a
novel instrument that we call the Centrifuge Force Microscope (CFM), in which
objects in an orbiting sample are subjected to a calibration-free,
macroscopically uniform force-field while their micro-to-nanoscopic motions are
observed. We demonstrate high-throughput single-molecule force spectroscopy
with this technique by performing thousands of rupture experiments in parallel,
characterizing force-dependent unbinding kinetics of an antibody-antigen pair
in minutes rather than days. Additionally, we verify the force accuracy of the
instrument by measuring the well-established DNA overstretching transition at
66 $\pm$ 3 pN. With significant benefits in efficiency, cost, simplicity, and
versatility, "single-molecule centrifugation" has the potential to
revolutionize single-molecule experimentation, and open access to a wider range
of researchers and experimental systems. | 10.1016/j.bpj.2010.03.012 |
|
2012-03-25T00:00:00 | Infrared lines, bands and plateaus in emission: from molecules to grains | Renaud Papoular | The IR emission spectra of molecules are deduced from the time variations of
their overall electric dipole moment. | null |
|
2012-12-03T00:00:00 | Advanced quantum methods for the largest magnetic molecules | J. Schnack, J. Ummethum | We discuss modern numerical methods for quantum spin systems and their
application to magnetic molecules. | Polyhedron 66 (2013) 28-33 | 10.1016/j.poly.2013.01.012 |
2013-08-04T00:00:00 | Elastic and inelastic collisions of $^2Σ$ molecules in a magnetic field | Jie Cui, Roman V. Krems | We calculate the cross sections for elastic scattering and Zeeman relaxation
in binary collisions of molecules in the ro-vibrational ground state of a
$^2\Sigma$ electronic state and the Zeeman state with the electron spin
projection $M_S=1/2$ on the magnetic field axis. This is the lowest-energy
state of $^2\Sigma$ molecules confined in a magnetic trap. The results are
averaged over calculations with multiple molecule - molecule interaction
potentials, which yields the expectation intervals for the cross sections and
the elastic-to-inelastic cross section ratios. We find that the
elastic-to-inelastic cross section ratios under conditions corresponding to
trapped molecular ensembles at $T \sim 10^{-3}$ K exceed 100 for the majority
of $^2\Sigma$ molecules. The range of $^2\Sigma$ molecules expected to be
collisionally unstable in magnetic traps at $T < 10^{-3}$ K is limited to
molecules with the spin-rotation interaction constant $\gamma_{\rm SR} > 0.5$
cm$^{-1}$ and the rotational constant $B_e < 4$ cm$^{-1}$. | 10.1103/PhysRevA.88.042705 |
|
2013-11-07T00:00:00 | All-optical sensing of a single-molecule electron spin | A. O. Sushkov, N. Chisholm, I. Lovchinsky, M. Kubo, P. K. Lo, S. D. Bennett, D. Hunger, A. Akimov, R. L. Walsworth, H. Park, M. D. Lukin | We demonstrate an all-optical method for magnetic sensing of individual
molecules in ambient conditions at room temperature. Our approach is based on
shallow nitrogen-vacancy (NV) centers near the surface of a diamond crystal,
which we use to detect single paramagnetic molecules covalently attached to the
diamond surface. The manipulation and readout of the NV centers is all-optical
and provides a sensitive probe of the magnetic field fluctuations stemming from
the dynamics of the electronic spins of the attached molecules. As a specific
example, we demonstrate detection of a single paramagnetic molecule containing
a gadolinium (Gd$^{3+}$) ion. We confirm single-molecule resolution using
optical fluorescence and atomic force microscopy to co-localize one NV center
and one Gd$^{3+}$-containing molecule. Possible applications include nanoscale
and in vivo magnetic spectroscopy and imaging of individual molecules. | 10.1021/nl502988n |
|
2013-11-14T00:00:00 | Examining resonant inelastic spontaneous scattering of classical Laguerre-Gauss beams from molecules | Aaron S. Rury | This paper theoretically treats the spontaneous resonant inelastic scattering
of Laguerre-Gauss (LG) beams from the totally symmetric vibrations of complex
polyatomic molecules within the semi-classical framework. We develop an
interaction Hamiltonian that accounts for the position of the molecule within
the excitation beam to derive the effective differential scattering
cross-section of a classical LG beam from a molecule using the frequency domain
third order nonlinear optical response function. To gain physical insight into
this scattering process, we utilize a model vibronic molecule to study the
changes to this scattering process. For specific molecular parameters including
vibrational frequency and relative displacement of the involved electronic
states, this investigation shows that an incident LG beam asymmetrically
enhances one of two participating excitation transitions causing modulation of
the interference present in the scattering process. This modulation allows a
pathway to coherent control of resonant inelastic scattering from complex,
poly-atomic molecules. We discuss the possible application of this control to
the resonant x-ray inelastic scattering (RIXS) of small poly-atomic molecules
central to applications ranging from single molecule electronics to solar
energy science. | Physical Review A, 87, 043408, (2013) | 10.1103/PhysRevA.87.043408 |
2015-04-23T00:00:00 | Effect of dipole polarizability on positron binding by strongly polar molecules | G. F. Gribakin, A. R. Swann | A model for positron binding to polar molecules is considered by combining
the dipole potential outside the molecule with a strongly repulsive core of a
given radius. Using existing experimental data on binding energies leads to
unphysically small core radii for all of the molecules studied. This suggests
that electron-positron correlations neglected in the simple model play a large
role in determining the binding energy. We account for these by including
polarization potential via perturbation theory and non-perturbatively. The
perturbative model makes reliable predictions of binding energies for a range
of polar organic molecules and hydrogen cyanide. The model also agrees with the
linear dependence of the binding energies on the polarizability inferred from
the experimental data [Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42
235203]. The effective core radii, however, remain unphysically small for most
molecules. Treating molecular polarization non-perturbatively leads to
physically meaningful core radii for all of the molecules studied and enables
even more accurate predictions of binding energies to be made for nearly all of
the molecules considered. | J. Phys. B 48, 215101 (2015) | 10.1088/0953-4075/48/21/215101 |
2015-10-26T00:00:00 | Asymmetric polycyclic aromatic hydrocarbon as a capable source of astronomically observed interstellar infrared spectrum | Norio Ota | In order to find out capable molecular source of astronomically well observed
infrared (IR) spectrum, asymmetric molecular configuration polycyclic aromatic
hydrocarbon (PAH) was analyzed by the density functional theory (DFT) analysis.
Starting molecules were benzene C6H6, naphthalene C10H8 and 1H-phenalene C13H9.
In interstellar space, those molecules will be attacked by high energy photon
and proton, which may bring cationic molecules as like C6H6n+ (n=0~3 in
calculation), C10H8n+, and C13H9n+, also CH lacked molecules C5H5n+, C9H7n+,
and C12H8n+. IR spectra of those molecules were analyzed based on DFT based
Gaussian program. Results suggested that symmetrical configuration molecules as
like benzene, naphthalene , 1H-phenalene and those cation ( +, 2+, and 3+) show
little resemblance with observed IR. Contrast to such symmetrical molecules,
several cases among cationic and asymmetric configuration molecules show fairly
good IR tendency. One typical example was C12H83+, of which calculated harmonic
IR wavelength were 3.2, 6.3, 7.5, 7.8, 8.7, 11.3, and 12.8 micro meter, which
correspond well to astronomically observed wavelength of 3.3, 6.2, 7.6, 7.8,
8.6, 11.2, and 12.7 micro meter. It was amazing agreement. Also, some cases
like C5H5+, C9H7+, C9H72+, C9H73+ and C12H82+ show fairly good coincidence.
Such results suggest that asymmetric and cationic PAH may be capable source of
interstellar dust. | null |
|
2018-04-30T00:00:00 | Conditional molecular design with deep generative models | Seokho Kang, Kyunghyun Cho | Although machine learning has been successfully used to propose novel
molecules that satisfy desired properties, it is still challenging to explore a
large chemical space efficiently. In this paper, we present a conditional
molecular design method that facilitates generating new molecules with desired
properties. The proposed model, which simultaneously performs both property
prediction and molecule generation, is built as a semi-supervised variational
autoencoder trained on a set of existing molecules with only a partial
annotation. We generate new molecules with desired properties by sampling from
the generative distribution estimated by the model. We demonstrate the
effectiveness of the proposed model by evaluating it on drug-like molecules.
The model improves the performance of property prediction by exploiting
unlabeled molecules, and efficiently generates novel molecules fulfilling
various target conditions. | Journal of Chemical Information and Modeling 59(1): 43-52, 2019 | 10.1021/acs.jcim.8b00263 |
2018-05-21T00:00:00 | Spin-State dependent Conductance Switching in Single Molecule-Graphene Junctions | Enrique Burzurí, Amador García-Fuente, Victor García-Suárez, Kuppusamy Senthil Kumar, Mario Ruben, Jaime Ferrer, Herre S. J. van der Zant | Spin-crossover (SCO) molecules are versatile magnetic switches with
applications in molecular electronics and spintronics. Downscaling devices to
the single-molecule level remains, however, a challenging task since the
switching mechanism in bulk is mediated by cooperative intermolecular
interactions. Here, we report on electron transport through individual Fe-SCO
molecules coupled to few-layer graphene electrodes \textit{via} $\pi - \pi$
stacking. We observe a distinct bistability in the conductance of the molecule
and a careful comparison with density functional theory (DFT) calculations
allows to associate the bistability with a SCO-induced orbital reconfiguration
of the molecule. We find long spin-state lifetimes that are caused by the
specific coordination of the magnetic core and the absence of intermolecular
interactions according to our calculations. In contrast with bulk samples, the
SCO transition is not triggered by temperature but induced by small
perturbations in the molecule at any temperature. We propose plausible
mechanisms that could trigger the SCO at the single-molecule level. | Nanoscale, 2018,10, 7905-7911 | 10.1039/C8NR00261D |
2010-03-10T00:00:00 | Ultracold giant polyatomic Rydberg molecules: coherent control of molecular orientation | Seth T. Rittenhouse, H. R. Sadeghpour | We predict the existence of a class of ultracold giant molecules formed from
trapped ultracold Rydberg atoms and polar molecules. The interaction which
leads to the formation of such molecules is the anisotropic charge-dipole
interaction ($a/R^2$). We show that prominent candidate molecules such as KRb
and deuterated hydroxyl (OD) should bind to Rydberg rubidium atoms, with
energies $E_b\simeq 5-25$ GHz at distances $R\simeq 0.1-1 \ \mu$m. These
molecules form in double wells, mimicking chiral molecules, with each well
containing a particular dipole orientation. We prepare a set of correlated
dressed electron-dipole eigenstates which are used in a resonant Raman scheme
to coherently control the dipole orientation and to create cat-like entangled
states of the polar molecule. | 10.1103/PhysRevLett.104.243002 |
|
2015-11-16T00:00:00 | Tip-Induced Molecule Anchoring in Ni-Phthalocyanine on Au(111) Substrate | Yong Chan Jeong, Sang Yong Song, Youngjae Kim, Youngtek Oh, Joongoo Kang, Jungpil Seo | Pinning single molecules at desired positions can provide opportunities to
fabricate bottom-up designed molecular machines. Using the combined approach of
scanning tunneling microscopy and density functional theory, we report on
tip-induced anchoring of Niphthalocyanine molecules on an Au(111) substrate. We
demonstrate that the tip-induced current leads to the dehydrogenation of a
benzene-like ligand in the molecule, which subsequently creates chemical bonds
between the molecule and the substrate. It is also found that the diffusivity
of Ni-phthalocyanine molecules is dramatically reduced when the molecules are
anchored on the Au adatoms produced by bias pulsing. The tip-induced molecular
anchoring would be readily applicable to other functional molecules that
contain similar ligands. | null |
|
2017-10-26T00:00:00 | Spin dynamics in helical molecules with non-linear interactions | E. Diaz, P. Albares, P. G. Estevez, J. M. Cervero, C. Gaul, E. Diez, F. Dominguez-Adame | It is widely admitted that the helical conformation of certain chiral
molecules may induce a sizable spin selectivity observed in experiments. Spin
selectivity arises as a result of the interplay between a helicity-induced
spin-orbit coupling and electric dipole fields in the molecule. From the
theoretical point of view, different phenomena might affect the spin dynamics
in helical molecules, such as quantum dephasing, dissipation and the role of
metallic contacts. Previous studies neglected the local deformation of the
molecule about the carrier thus far, but this assumption seems unrealistic to
describe charge transport in molecular systems. We introduce an effective model
describing the electron spin dynamics in a deformable helical molecule with
weak spin-orbit coupling. We find that the electron-lattice interaction allows
the formation of stable solitons such as bright solitons with well defined spin
projection onto the molecule axis. We present a thorough study of these bright
solitons and analyze their possible impact on the spin dynamics in deformable
helical molecules. | 10.1088/1367-2630/aabb91 |
|
2016-01-18T00:00:00 | Pulling Platinum Atomic Chains by Carbon Monoxide Molecules | Péter Makk, Zoltán Balogh, Szabolcs Csonka, András Halbritter | The interaction of carbon monoxide molecules with atomic-scale platinum
nanojunctions is investigated by low temperature mechanically controllable
break junction experiments. Combining plateaus' length analysis, two
dimensional conductance-displacement histograms and conditional correlation
analysis a comprehensive microscopic picture is proposed about the formation
and evolution of Pt-CO-Pt single-molecule configurations. Our analysis implies
that before pure Pt monoatomic chains would be formed a CO molecule infiltrates
the junction, first in a configuration being perpendicular to the contact axis.
This molecular junction is strong enough to pull a monoatomic platinum chain
with the molecule being incorporated in the chain. Along the chain formation
the molecule can either stay in the perpendicular configuration, or rotate to a
parallel configuration. The evolution of the single-molecule configurations
along the junction displacement shows quantitative agreement with theoretical
predictions, justifying the interpretation in terms of perpendicular and
parallel molecular alignment. Our analysis demonstrates that the combination of
two dimensional conductance-displacement histograms with conditional
correlation analysis is a useful tool to separately analyze fundamentally
different types of junction trajectories in single molecule break junction
experiments. | Nanoscale, 4, 4739-4745 (2012) | 10.1039/c2nr30832k |
2018-07-30T00:00:00 | Observation of magnetically tunable Feshbach resonances in ultracold $^{23}$Na$^{40}$K+$^{40}$K collisions | Huan Yang, De-Chao Zhang, Lan Liu, Ya-Xiong Liu, Jue Nan, Bo Zhao, Jian-Wei Pan | Resonances in ultracold collisions involving heavy molecules are difficult to
understand, and have proven challenging to detect. Here we report the
observation of magnetically tunable Feshbach resonances in ultracold collisions
between $^{23}$Na$^{40}$K molecules in the rovibrational ground state and
$^{40}$K atoms. We prepare the atoms and molecules in various hyperfine levels
of their ground states and observe the loss of molecules as a function of the
magnetic field. The atom-molecule Feshbach resonances are identified by
observing an enhancement of the loss rate coefficients. We have observed three
resonances at approximately 101 G in various atom-molecule scattering channels,
with the widths being a few hundred milliGauss. The observed atom-molecule
Feshbach resonances at ultralow temperatures probe the three-body potential
energy surface with an unprecedented resolution. Our work will help to improve
the understanding of complicated ultracold collisions, and open up the
possibility of creating ultracold triatomic molecules. | 10.1126/science.aau5322 |
|
2017-11-14T00:00:00 | Molecular Configuration Around Single Vacancy in Solid CO2 at T = 0 K Studied by Monte Carlo Simulation Technique | Koji Kobashi | Energetically minimum configurations of the first- and second-nearest
neighbor (NN) CO2 molecules surrounding a vacancy, created by removing a single
molecule from the Pa3 structure, were calculated by use of the Monte Carlo
simulation technique at zero temperature. It was found that among the 1st NN
molecules, only six NN molecules, closest to the oxygen atoms of the removed
CO2 molecule, significantly changed the positions and orientations, while the
other six molecules were not influenced by the creation of the vacancy. The
configurations of the molecules no longer had the three-fold symmetry that the
Pa3 structure possessed. The influence of the vacancy on the 2nd NN molecules
was relatively small. | null |
|
2014-06-14T00:00:00 | Raman Images of a Single Molecule in a Highly Confined Plasmonic Field | Sai Duan, Guangjun Tian, Yongfei Ji, Jiushu Shao, Zhenchao Dong, Yi Luo | Under the local plasmonic excitation, the Raman images of a single molecule
can now reach sub-nanometer resolution. We report here a theoretical
description of the interaction between a molecule and a highly confined
plasmonic field. It is shown that when the spatial distribution of the
plasmonic field is comparable with the size of the molecule, the optical
transition matrix of the molecule becomes to be dependent on the position and
the spatial distribution of the plasmonic field, resulting in spatially
resolved Raman image of a molecule. It is found that the resonant Raman image
reflects the electronic transition density of the molecule. In combination with
the first principles calculations, the simulated Raman image of a porphyrin
derivative adsorbed on the silver surface nicely reproduces its experimental
counterpart. The present theory provides the basic framework for describing
linear and nonlinear responses of molecules under the highly confined plasmonic
field. | J. Am. Chem. Soc., 2015, 137 (30), pp 9515-9518 | 10.1021/jacs.5b03741 |
2014-06-18T00:00:00 | Quantum magnetism with ultracold molecules | M. L. Wall, K. R. A. Hazzard, A. M. Rey | This article gives an introduction to the realization of effective quantum
magnetism with ultracold molecules in an optical lattice, reviews experimental
and theoretical progress, and highlights future opportunities opened up by
ongoing experiments. Ultracold molecules offer capabilities that are otherwise
difficult or impossible to achieve in other effective spin systems, such as
long-ranged spin-spin interactions with controllable degrees of spatial and
spin anisotropy and favorable energy scales. Realizing quantum magnetism with
ultracold molecules provides access to rich many-body behaviors, including many
exotic phases of matter and interesting excitations and dynamics.
Far-from-equilibrium dynamics plays a key role in our exposition, just as it
did in recent ultracold molecule experiments realizing effective quantum
magnetism. In particular, we show that dynamical probes allow the observation
of correlated many-body spin physics, even in polar molecule gases that are not
quantum degenerate. After describing how quantum magnetism arises in ultracold
molecules and discussing recent observations of quantum magnetism with polar
molecules, we survey prospects for the future, ranging from immediate goals to
long-term visions. | 10.1142/9789814678704_0001 |
|
2014-10-15T00:00:00 | Realizing unconventional quantum magnetism with symmetric top molecules | M. L. Wall, K. Maeda, L. D. Carr | We demonstrate that ultracold symmetric top molecules loaded into an optical
lattice can realize highly tunable and unconventional models of quantum
magnetism, such as an XYZ Heisenberg spin model. We show that anisotropic
dipole-dipole interactions between molecules can lead to effective spin-spin
interactions which exchange spin and orbital angular momentum. This exchange
produces effective spin models which do not conserve magnetization and feature
tunable degrees of spatial and spin-coupling anisotropy. In addition to
deriving pure spin models when molecules are pinned in a deep optical lattice,
we show that models of itinerant magnetism are possible when molecules can
tunnel through the lattice. Additionally, we demonstrate rich tunability of the
effective models' parameters using only a single microwave frequency, in
contrast to proposals with $^1\Sigma$ diatomic molecules, which often require
many microwave frequencies. Our results are germane not only for experiments
with polyatomic symmetric top molecules, such as methyl fluoride (CH$_3$F), but
also diatomic molecules with an effective symmetric top structure, such as the
hydroxyl radical OH. | New J. Phys. 17 025001 (2015) | 10.1088/1367-2630/17/2/025001 |
2019-11-23T00:00:00 | CORE: Automatic Molecule Optimization Using Copy & Refine Strategy | Tianfan Fu, Cao Xiao, Jimeng Sun | Molecule optimization is about generating molecule $Y$ with more desirable
properties based on an input molecule $X$. The state-of-the-art approaches
partition the molecules into a large set of substructures $S$ and grow the new
molecule structure by iteratively predicting which substructure from $S$ to
add. However, since the set of available substructures $S$ is large, such an
iterative prediction task is often inaccurate especially for substructures that
are infrequent in the training data. To address this challenge, we propose a
new generating strategy called "Copy & Refine" (CORE), where at each step the
generator first decides whether to copy an existing substructure from input $X$
or to generate a new substructure, then the most promising substructure will be
added to the new molecule. Combining together with scaffolding tree generation
and adversarial training, CORE can significantly improve several latest
molecule optimization methods in various measures including drug likeness
(QED), dopamine receptor (DRD2) and penalized LogP. We tested CORE and
baselines using the ZINC database and CORE obtained up to 11% and 21%
relatively improvement over the baselines on success rate on the complete test
set and the subset with infrequent substructures, respectively. | null |
|
2019-12-18T00:00:00 | Theoretical Investigations of Electronic Structure, Magnetic and Optical Properties of Transition Metal-dinuclear Molecules | Indukuru Ramesh Reddy, Kartick Tarafder | The work presents the electronic structure, spin state and optical properties
of TM-dinuclear molecules (TM = Cr, Mn, Fe, Co, and Ni) which was modelled
according to the recently reported Pt$^{II}$-dinuclear complex
data\cite{kar_colour_2016}. The molecules were geometrically optimized in the
gas phase and their stability were analyzed from vibrational spectra study
using density functional theory (DFT) calculations. The ground spin state of
the tetra-coordinated TM atom in the modeled molecules was predicted based on
the relative energies between the possible spin states of the molecules. We
further performed DFT+U calculations to investigate the precise ground state
spin configuration of molecules. Interestingly, optical characterization of
these molecules shows that the absorption spectra have a large peak in the
blue-light wavelength range, therefore could be suitable for blue-LED
application. Our work promotes further computational and experimental studies
on TM-dinuclear molecules in field of molecular spintronics and
optoelectronics. | null |
|
2019-12-19T00:00:00 | Collision dynamics and reactions of fractional vortex molecules in coherently coupled Bose-Einstein condensates | Minoru Eto, Kazuki Ikeno, Muneto Nitta | Coherently coupled two-component Bose-Einstein condensates (BEC) exhibit
vortex confinement resembling quark confinement in Quantum Chromo Dynamics
(QCD). Fractionally quantized vortices winding only in one of two components
are attached by solitons, and they cannot stably exist alone. Possible stable
states are "hadrons" either of mesonic type, i.e., molecules made of a vortex
and anti-vortex in the same component connected by a soliton, or of baryonic
type, i.e., molecules made of two vortices winding in two different components
connected by a soliton. Mesonic molecules move straight with a constant
velocity while baryonic molecules rotate. We numerically simulate collision
dynamics of mesonic and baryonic molecules and find that the molecules swap a
partner in collisions in general like chemical and nuclear reactions, summarize
all collisions as vortex reactions, and describe those by Feynman diagrams. We
find a selection rule for final states after collisions of vortex molecules,
analogous to that for collisions of hadrons in QCD. | Phys. Rev. Research 2, 033373 (2020) | 10.1103/PhysRevResearch.2.033373 |
2011-02-09T00:00:00 | Optimal trapping wavelengths of Cs$_2$ molecules in an optical lattice | Romain Véxiau, Nadia Bouloufa, Mireille Aymar, Johann Georg Danzl, Manfred J Mark, Hans-Christoph Naegerl, Olivier Dulieu | The present paper aims at finding optimal parameters for trapping of Cs$_2$
molecules in optical lattices, with the perspective of creating a quantum
degenerate gas of ground-state molecules. We have calculated dynamic
polarizabilities of Cs$_2$ molecules subject to an oscillating electric field,
using accurate potential curves and electronic transition dipole moments. We
show that for some particular wavelengths of the optical lattice, called "magic
wavelengths", the polarizability of the ground-state molecules is equal to the
one of a Feshbach molecule. As the creation of the sample of ground-state
molecules relies on an adiabatic population transfer from weakly-bound
molecules created on a Feshbach resonance, such a coincidence ensures that both
the initial and final states are favorably trapped by the lattice light,
allowing optimized transfer in agreement with the experimental observation. | 10.1140/epjd/e2011-20085-4 |
|
2013-10-31T00:00:00 | Spatial Imaging of Landé g Factor through Extended Kondo Effect in a Single Magnetic Molecule | Liwei Liu, Yuhang Jiang, Boqun Song, Kai Yang, Wende Xiao, Shixuan Du, Min Ouyang, Werner A. Hofer, Antonio. H. Castro Neto, Hong-Jun Gao | A methodology of atomically resolved Land\'{e} g factor mapping of a single
molecule is reported. Mn(II)-phthalocyanine (MnPc) molecules on Au(111) surface
can be dehydrogenated via atomic manipulation with manifestation of tailored
extended Kondo effect, which can allow atomically resolved imaging of the
Land\'{e} g factor inside a molecule for the first time. By employing
dehydrogenated MnPc molecules with removal of six H atoms (-6H-MnPc) as an
example, Land\'{e} g factor of atomic constituents of the molecule can be
obtained, therefore offering a unique g factor mapping of single molecule. Our
results open up a new avenue to access local spin texture of a single molecule. | null |
|
2014-12-23T00:00:00 | Tuning the magnetic anisotropy of single molecules | Benjamin W. Heinrich, Lukas Braun, Jose I. Pascual, Katharina J. Franke | The magnetism of single atoms and molecules is governed by the atomic scale
environment. In general, the reduced symmetry of the surrounding splits the $d$
states and aligns the magnetic moment along certain favorable directions. Here,
we show that we can reversibly modify the magnetocrystalline anisotropy by
manipulating the environment of single iron(II) porphyrin molecules adsorbed on
Pb(111) with the tip of a scanning tunneling microscope. When we decrease the
tip--molecule distance, we first observe a small increase followed by an
exponential decrease of the axial anisotropy on the molecules. This is in
contrast to the monotonous increase observed earlier for the same molecule with
an additional axial Cl ligand. We ascribe the changes in the anisotropy of both
species to a deformation of the molecules in the presence of the attractive
force of the tip, which leads to a change in the $d$ level alignment. These
experiments demonstrate the feasibility of a precise tuning of the magnetic
anisotropy of an individual molecule by mechanical control. | Nano Lett. 15, 4024 (2015) | 10.1021/acs.nanolett.5b00987 |
2019-06-24T00:00:00 | Performance Enhancement of Diffusion-based Molecular Communication with Photolysis | Oussama A. Dambri, Soumaya Cherkaoui | Inter-Symbol Interference (ISI) is the main challenge of bio-inspired
diffusion-based molecular communication. In real biological systems, the
degradation of the remaining molecules from a previous transmission is used to
mitigate ISI. While most prior works have proposed the use of enzymes to
catalyze the molecule degradation, enzymes also degrade the molecules carrying
the information, which drastically decreases the signal strength. In this
paper, we propose the use of photolysis reactions, which use the light to
instantly transform the emitted molecules so they are no longer recognized
after their detection. The light is emitted at an optimal time, allowing the
receiver to detect as many molecules as possible, which increases both the
signal strength and ISI mitigation. A lower bound expression on the expected
number of the observed molecules at the receiver is derived. The bit error
probability expression is also formulated. Both the expected number of observed
molecules and the bit error expressions are validated with simulation results,
which show a visible enhancement when using photolysis reactions. The
performance of the proposed method is evaluated using the
Interference-to-Total-Received molecules metric (ITR) and the derived bit error
probability. | null |
|
2020-07-13T00:00:00 | Ultralong-range Rydberg bi-molecules | Rosario Gonzalez-Ferez, Janine Shertzer, H. R. Sadeghpour | We predict that ultralong-range Rydberg bi-molecules form in collisions
between polar molecules in cold and ultracold settings. The collision of
$\Lambda$-doublet nitric oxide (NO) with long-lived Rydberg NO($nf$, $ng$)
molecules forms ultralong-range Rydberg bi-molecules with GHz energies and
kilo-Debye permanent electric dipole moments. The Hamiltonian includes both the
anisotropic charge-molecular dipole interaction and the electron-NO scattering.
The rotational constant for the Rydberg bi-molecules is in the MHz range,
allowing for microwave spectroscopy of rotational transitions in Rydberg
bi-molecules. Considerable orientation of NO dipole can be achieved. The
Rydberg molecules described here hold promise for studies of a special class of
long-range bi-molecular interactions. | Phys. Rev. Lett. 126, 043401 (2021) | 10.1103/PhysRevLett.126.043401 |
2020-08-07T00:00:00 | Polyatomic Molecules as Quantum Sensors for Fundamental Physics | Nicholas R. Hutzler | Precision measurements in molecules have advanced rapidly in recent years
through developments in techniques to cool, trap, and control. The complexity
of molecules makes them a challenge to study, but also offers opportunities for
enhanced sensitivity to many interesting effects. Polyatomic molecules offer
additional complexity compared to diatomic molecules, yet are still "simple"
enough to be laser-cooled and controlled. While laser cooling molecules is
still a research frontier itself, there are many proposed and ongoing
experiments seeking to combine the advanced control enabled by ultracold
temperatures with the intrinsic sensitivity of molecules. In this perspective,
we discuss some applications where laser-cooled polyatomic molecules may offer
advantages for precision measurements of fundamental physics, both within and
beyond the Standard Model. | Quantum Science and Technology 5, 044011 (2020) | 10.1088/2058-9565/abb9c5 |
2020-09-16T00:00:00 | Selective Conduction of Organic Molecules via Free-Standing Graphene | Zhao Wang | A race is held between ten species of organic gas molecules on a graphene
substrate driven by thermal gradients via molecular dynamics. Fast conduction
of the molecules is observed with selectivity for aromatic compounds. This
selectivity stems from the fact that the planar structure of the aromatic
molecule helps keep a shorter distance to the substrate, which is the key to
the driving force at the gas-solid interface. The drift velocity monotonically
increases with decreasing molecule density, with no ballistic transport
observable even for a single molecule. A non-linear regime is discovered for
the conduction of benzene molecules under large thermal gradients. At low
temperature, molecules formed aggregation and move collectively along specific
path in the graphene substrate. | J. Phys. Chem. C 123, 15166-15170 (2019) | 10.1021/acs.jpcc.9b04131 |
2020-10-19T00:00:00 | Learning Latent Space Energy-Based Prior Model for Molecule Generation | Bo Pang, Tian Han, Ying Nian Wu | Deep generative models have recently been applied to molecule design. If the
molecules are encoded in linear SMILES strings, modeling becomes convenient.
However, models relying on string representations tend to generate invalid
samples and duplicates. Prior work addressed these issues by building models on
chemically-valid fragments or explicitly enforcing chemical rules in the
generation process. We argue that an expressive model is sufficient to
implicitly and automatically learn the complicated chemical rules from the
data, even if molecules are encoded in simple character-level SMILES strings.
We propose to learn latent space energy-based prior model with SMILES
representation for molecule modeling. Our experiments show that our method is
able to generate molecules with validity and uniqueness competitive with
state-of-the-art models. Interestingly, generated molecules have structural and
chemical features whose distributions almost perfectly match those of the real
molecules. | null |
|
2020-11-25T00:00:00 | RetroGNN: Approximating Retrosynthesis by Graph Neural Networks for De Novo Drug Design | Cheng-Hao Liu, Maksym Korablyov, Stanisław Jastrzębski, Paweł Włodarczyk-Pruszyński, Yoshua Bengio, Marwin H. S. Segler | De novo molecule generation often results in chemically unfeasible molecules.
A natural idea to mitigate this problem is to bias the search process towards
more easily synthesizable molecules using a proxy for synthetic accessibility.
However, using currently available proxies still results in highly unrealistic
compounds. We investigate the feasibility of training deep graph neural
networks to approximate the outputs of a retrosynthesis planning software, and
their use to bias the search process. We evaluate our method on a benchmark
involving searching for drug-like molecules with antibiotic properties.
Compared to enumerating over five million existing molecules from the ZINC
database, our approach finds molecules predicted to be more likely to be
antibiotics while maintaining good drug-like properties and being easily
synthesizable. Importantly, our deep neural network can successfully filter out
hard to synthesize molecules while achieving a $10^5$ times speed-up over using
the retrosynthesis planning software. | null |
|
2021-01-15T00:00:00 | Revising Berg-Purcell for finite receptor kinetics | Gregory Handy, Sean D Lawley | From nutrient uptake, to chemoreception, to synaptic transmission, many
systems in cell biology depend on molecules diffusing and binding to membrane
receptors. Mathematical analysis of such systems often neglects the fact that
receptors process molecules at finite kinetic rates. A key example is the
celebrated formula of Berg and Purcell for the rate that cell surface receptors
capture extracellular molecules. Indeed, this influential result is only valid
if receptors transport molecules through the cell wall at a rate much faster
than molecules arrive at receptors. From a mathematical perspective, ignoring
receptor kinetics is convenient because it makes the diffusing molecules
independent. In contrast, including receptor kinetics introduces correlations
between the diffusing molecules since, for example, bound receptors may be
temporarily blocked from binding additional molecules. In this work, we present
a modeling framework for coupling bulk diffusion to surface receptors with
finite kinetic rates. The framework uses boundary homogenization to couple the
diffusion equation to nonlinear ordinary differential equations on the
boundary. We use this framework to derive an explicit formula for the cellular
uptake rate and show that the analysis of Berg and Purcell significantly
overestimates uptake in some typical biophysical scenarios. We confirm our
analysis by numerical simulations of a many particle stochastic system. | 10.1016/j.bpj.2021.03.021 |
|
2021-02-07T00:00:00 | Simulation electronic thermes of two atoms molecules | Vladimir Koshcheev, Yuriy Shtanov | In the first order of the perturbation theory, the correction to the
electronic terms of a diatomic molecule is calculated taking into account the
Pauli principle. | null |
|
2021-02-22T00:00:00 | Feynman-Enderlein Path Integral for Single-Molecule Nanofluidics | Siddharth Ghosh | Single-molecule motions in the nanofluidic domain are extremely difficult to
characterise because of various complex physical and physicochemical
interactions. We present a method for quasi-one-dimensional
sub-diffraction-limited nanofluidic motions of fluorescent single molecules
using the Feynman-Enderlein path integral approach. This theory was validated
using the Monte Carlo simulation to provide fundamental understandings of
single-molecule nanofluidic flow and diffusion in liquid. The distribution of
single-molecule burst size can be precise enough to detect molecular
interaction. The realisation of this theoretical study considers several
fundamental aspects of single-molecule nanofluidics, such as electrodynamics,
photophysics, and multi-molecular events/molecular shot noise. We study
{molecules within (an order of magnitude of) realistic lengthscale for organic
molecules, biomolecules, and nanoparticles where 1.127~nm and 11.27~nm
hydrodynamic radii of molecules were driven by a wide range of flow velocities
ranging from $0.01~\mu$m/s to $10~\mu$m/s. It is the first study to report
distinctly different velocity-dependent nanofluidic regimes. | null |
|
2021-05-22T00:00:00 | Spin Seebeck effect of correlated magnetic molecules | Anand Manaparambil, Ireneusz Weymann | In this paper we investigate the spin-resolved thermoelectric properties of
strongly correlated molecular junctions in the linear response regime. The
magnetic molecule is modeled by a single orbital level to which the molecular
core spin is attached by an exchange interaction. Using the numerical
renormalization group method we analyze the behavior of the (spin) Seebeck
effect, heat conductance and figure of merit for different model parameters of
the molecule. We show that the thermopower strongly depends on the strength and
type of the exchange interaction as well as the molecule's magnetic anisotropy.
When the molecule is coupled to ferromagnetic leads, the thermoelectric
properties reveal an interplay between the spin-resolved tunneling processes
and intrinsic magnetic properties of the molecule. Moreover, in the case of
finite spin accumulation in the leads, the system exhibits the spin Seebeck
effect. We demonstrate that a considerable spin Seebeck effect can develop when
the molecule exhibits an easy-plane magnetic anisotropy, while the sign of the
spin thermopower depends on the type and magnitude of the molecule's exchange
interaction. | Sci. Rep. 11, 1 (2021) | 10.1038/s41598-021-88373-7 |
2021-12-02T00:00:00 | An optical tweezer array of ground-state polar molecules | Jessie T. Zhang, Lewis R. B. Picard, William B. Cairncross, Kenneth Wang, Yichao Yu, Fang Fang, Kang-Kuen Ni | Fully internal and motional state controlled and individually manipulable
polar molecules are desirable for many quantum science applications leveraging
the rich state space and intrinsic interactions of molecules. While prior
efforts at assembling molecules from their constituent atoms individually
trapped in optical tweezers achieved such a goal for exactly one molecule, here
we extend the technique to an array of five molecules, unlocking the ability to
study molecular interactions. We detail the technical challenges and solutions
inherent in scaling this system up. With parallel preparation and control of
multiple molecules in hand, this platform now serves as a starting point to
harness the vast resources and long-range dipolar interactions of molecules. | null |
|
2022-04-25T00:00:00 | Translation between Molecules and Natural Language | Carl Edwards, Tuan Lai, Kevin Ros, Garrett Honke, Kyunghyun Cho, Heng Ji | We present $\textbf{MolT5}$ $-$ a self-supervised learning framework for
pretraining models on a vast amount of unlabeled natural language text and
molecule strings. $\textbf{MolT5}$ allows for new, useful, and challenging
analogs of traditional vision-language tasks, such as molecule captioning and
text-based de novo molecule generation (altogether: translation between
molecules and language), which we explore for the first time. Since
$\textbf{MolT5}$ pretrains models on single-modal data, it helps overcome the
chemistry domain shortcoming of data scarcity. Furthermore, we consider several
metrics, including a new cross-modal embedding-based metric, to evaluate the
tasks of molecule captioning and text-based molecule generation. Our results
show that $\textbf{MolT5}$-based models are able to generate outputs, both
molecules and captions, which in many cases are high quality. | null |
|
2022-06-30T00:00:00 | Structural aspects of the clustering of curcumin molecules in water. Molecular dynamics computer simulation study | T. Patsahan, O. Pizio | We explore clustering of curcumin molecules in water by using the OPLS-UA
model for the enol conformer of curcumin (J. Mol. Liq., \textbf{223}, 707,
2016) and the SPC-E water model. With this purpose, solutions of 2, 4, 8, 12,
16 and 20 curcumin molecules in 3000 water molecules are studied by using
extensive molecular dynamics computer simulations. Radial distributions for the
centers of mass of curcumin molecules are evaluated and the running
coordination numbers are analyzed. The formation of clusters on time is
elucidated. The internal structure of molecules within the cluster is described
by using radial distributions of the elements of the curcumin molecule, the
orientation descriptors, the order parameter and the radius of gyration. The
self-diffusion coefficient of solute molecules in clusters is evaluated. The
distribution of water species around clusters is described in detail. A
comparison of our findings with computer simulation results of other authors is
performed. A possibility to relate predictions of the model with experimental
observations is discussed. | Condensed Matter Physics, 2021, vol. 25, No. 2, 23201 | 10.5488/CMP.25.23201 |
2022-07-04T00:00:00 | High-throughput property-driven generative design of functional organic molecules | Julia Westermayr, Joe Gilkes, Rhyan Barrett, Reinhard J. Maurer | The design of molecules and materials with tailored properties is
challenging, as candidate molecules must satisfy multiple competing
requirements that are often difficult to measure or compute. While molecular
structures, produced through generative deep learning, will satisfy those
patterns, they often only possess specific target properties by chance and not
by design, which makes molecular discovery via this route inefficient. In this
work, we predict molecules with (pareto)-optimal properties by combining a
generative deep learning model that predicts three dimensional conformations of
molecules with a supervised deep learning model that takes these as inputs and
predicts their electronic structure. Optimization of (multiple) molecular
properties is achieved by screening newly generated molecules for desirable
electronic properties and reusing hit molecules to retrain the generative model
with a bias. The approach is demonstrated to find optimal molecules for organic
electronics applications. Our method is generally applicable and eliminates the
need for quantum chemical calculations during predictions, making it suitable
for high-throughput screening in materials and catalyst design. | Nature Computational Science (2023) | 10.1038/s43588-022-00391-1 |
2022-08-27T00:00:00 | On the influence of Maxwell--Chern--Simons electrodynamics in nuclear fusion involving electronic and muonic molecules | Francisco Caruso, Vitor Oguri, Felipe Silveira, Amos Troper | New results recently obtained (\textit{Annals of Physics} (New York)
a.n.~168943) established some non-relativistic ground state solutions for
three-body molecules interacting through a Chern--Simons model. Within this
model, it was argued that Chern--Simons potential should not help improve the
fusion rates by replacing electrons with muons, in the case of particular
muonic molecules. This achievement motivated us to investigate quantitatively
whether or not the Maxwell--Chern--Simons electrodynamics could influence
positively, for example, the probability of having a muon-catalyzed fusion; its
contribution to electronic molecules is also considered in this letter. The
principal factors related to the probability of elementary nuclear fusion are
therefore numerically calculated and compared with their analogs admitting
other forms of interaction like $-1/\rho$ and $\ln (\rho)$. The analysis
carried on here confirms that one should not expect a significant improvement
in nuclear fusion rates in the case of muonic molecules, although,
surprisingly, the same is not true for electronic molecules, compared with
other theoretical predictions. Numerical predictions for the fusion rates for
$ppe$, $pp\mu$, $dde$ and $dd\mu$ molecules are given as well as the predicted
value for the tunneling rate for these molecules. | 10.1209/0295-5075/aca2d4 |
|
2022-09-20T00:00:00 | Probabilistic Generative Transformer Language models for Generative Design of Molecules | Lai Wei, Nihang Fu, Yuqi Song, Qian Wang, Jianjun Hu | Self-supervised neural language models have recently found wide applications
in generative design of organic molecules and protein sequences as well as
representation learning for downstream structure classification and functional
prediction. However, most of the existing deep learning models for molecule
design usually require a big dataset and have a black-box architecture, which
makes it difficult to interpret their design logic. Here we propose Generative
Molecular Transformer (GMTransformer), a probabilistic neural network model for
generative design of molecules. Our model is built on the blank filling
language model originally developed for text processing, which has demonstrated
unique advantages in learning the "molecules grammars" with high-quality
generation, interpretability, and data efficiency. Benchmarked on the MOSES
datasets, our models achieve high novelty and Scaf compared to other baselines.
The probabilistic generation steps have the potential in tinkering molecule
design due to their capability of recommending how to modify existing molecules
with explanation, guided by the learned implicit molecule chemistry. The source
code and datasets can be accessed freely at
https://github.com/usccolumbia/GMTransformer | null |
|
2022-11-13T00:00:00 | Enantiomer detection via Quantum Otto cycle | Mohsen Izadyari, M. Tahir Naseem, Özgür E. Müstecaplıouglu | Enantiomers are chiral molecules that exist in right-handed and left-handed
conformations. Optical techniques of enantiomers detection are widely employed
to discriminate between left- and right-handed molecules. However, identical
spectra of enantiomers make enantiomer detection a very challenging task. Here,
we investigate the possibility of exploiting thermodynamic processes for
enantiomer detection. In particular, we employ a quantum Otto cycle, in which a
chiral molecule described by a three-level system with cyclic optical
transitions is considered a working medium. Each energy transition of the
three-level system is coupled with an external laser drive. We find that the
left-handed molecule works as a heat engine, while the right-handed molecule
works as a thermal accelerator where the overall phase of the drives is
considered as the cycle's control parameter. In addition, both left- and
right-handed molecules work as heat engines by considering laser drives'
detuning as the control parameter. However, the molecules can still be
distinguished because both cases' extracted work and efficiency are
quantitatively very different. Accordingly, left and right-handed molecules can
be distinguished by evaluating the work distribution in the Otto cycle. | null |
|
2022-11-20T00:00:00 | Magnetic trapping of ultracold molecules at high density | Juliana J. Park, Yu-Kun Lu, Alan O. Jamison, Wolfgang Ketterle | Trapping ultracold molecules in conservative traps is essential for
applications -- such as quantum state-controlled chemistry, quantum
simulations, and quantum information processing. These applications require
high densities or phase-space densities. We report magnetic trapping of NaLi
molecules in the triplet ground state at high density ($\approx 10^{11} \;
\rm{cm}^{-3}$) and ultralow temperature ($\approx 1\;{\rm \mu K}$). Magnetic
trapping at these densities allows studies on both atom-molecule and
molecule-molecule collisions in the ultracold regime in the absence of trapping
light, which has often lead to undesired photo-chemistry. We measure the
inelastic loss rates in a single spin sample and spin-mixtures of fermionic
NaLi as well as spin-stretched NaLi$+$Na mixtures. We demonstrate sympathetic
cooling of NaLi molecules in the magnetic trap by radio frequency evaporation
of co-trapped Na atoms and observe an increase in the molecules' phase-space
density by a factor of $\approx 16$. | null |
|
2022-11-24T00:00:00 | Laser cooling of molecules | Eunmi Chae | A recent progress on laser cooling of molecules is summarized. Since the
development during 1980s for atomic species, laser cooling has been the very
beginning step to cool and trap atoms for frontier research on quantum
simulations, quantum sensing and precision measurements. Despite the complex
internal structures of molecules, laser cooling of molecules have been realized
with the deepened understanding of molecular structures and interaction between
light and molecules. The development of laser technology over the last decades
have also been a great aid for laser cooling of molecules because many lasers
are necessary to successfully cool the molecules. A detailed principle and
development of laser cooling of molecules as well as the current status of the
field are reviewed to give an introductory of the growing field of ultracold
molecular physics. | null |
|
2022-12-17T00:00:00 | Molecule optimization via multi-objective evolutionary in implicit chemical space | Xin Xia, Yansen Su, Chunhou Zheng, Xiangxiang Zeng | Machine learning methods have been used to accelerate the molecule
optimization process. However, efficient search for optimized molecules
satisfying several properties with scarce labeled data remains a challenge for
machine learning molecule optimization. In this study, we propose MOMO, a
multi-objective molecule optimization framework to address the challenge by
combining learning of chemical knowledge with Pareto-based multi-objective
evolutionary search. To learn chemistry, it employs a self-supervised codec to
construct an implicit chemical space and acquire the continues representation
of molecules. To explore the established chemical space, MOMO uses
multi-objective evolution to comprehensively and efficiently search for similar
molecules with multiple desirable properties. We demonstrate the high
performance of MOMO on four multi-objective property and similarity
optimization tasks, and illustrate the search capability of MOMO through case
studies. Remarkably, our approach significantly outperforms previous approaches
in optimizing three objectives simultaneously. The results show the
optimization capability of MOMO, suggesting to improve the success rate of lead
molecule optimization. | null |
|
2023-02-20T00:00:00 | Direct Laser Cooling of Polyatomic Molecules | Benjamin L. Augenbraun, Loic Anderegg, Christian Hallas, Zack D. Lasner, Nathaniel B. Vilas, John M. Doyle | Over the past decade, tremendous progress has been made to extend the tools
of laser cooling and trapping to molecules. Those same tools have recently been
applied to polyatomic molecules (molecules containing three or more atoms). In
this review, we discuss the scientific drive to bring larger molecules to
ultralow temperatures, the features of molecular structure that provide the
most promising molecules for this pursuit, and some technical aspects of how
lasers can be used to control the motion and quantum states of polyatomic
molecules. We also present opportunities for and challenges to the use of
polyatomic molecules for science and technology. | null |
|
2001-11-13T00:00:00 | Critical Temperature Tc versus Charging Energy Ec in Molecular-Intercalated Fullerenes | Chikao Kawabata, Nobuhiko Hayashi, Fumihisa Ono | We study the recently discovered 117-Kelvin superconducting system C60/CHBr3
of the field-effect transistor and propose a possibility that the intercalation
molecule CHBr3 plays a role of an electric capacitor in the C60 fullerene
superconductor, which contrasts rather with an expectation that the
intercalation molecule in that system acts as simple spacer molecule.
Estimating the critical temperatures Tc for several C60/X (X: intercalation
molecule), we suggest searching for intercalation molecules with large
molecular polarizabilities, in order to attain higher Tc in the synthesis of
fullerene superconductors and to more systematically develop high Tc
superconducting electronic devices. | null |
|
2002-03-26T00:00:00 | Towards the molecular workshop: entropy-driven designer molecules, entropy activation, and nanomechanical devices | Andreas Hanke, Ralf Metzler | We introduce some basic concepts for designer molecules with functional units
which are driven by entropic rather than energetic forces. This idea profits
from the mechanically interlocked nature of topological molecules such as
catenanes and rotaxanes, which allows for mobile elements whose accessible
configuration space gives rise to entropic intramolecular forces. Such
entropy-driven designer molecules open the possibility for externally
controllable functional molecules and nanomechanical devices. | 10.1016/S0009-2614(02)00675-9 |
|
2002-06-13T00:00:00 | Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping | S. Cocco, J. F. Marko, R. Monasson | We review statistical-mechanical theories of single-molecule
micromanipulation experiments on nucleic acids. First, models for describing
polymer elasticity are introduced. We then review how these models are used to
interpret single-molecule force-extension experiments on single-stranded and
double-stranded DNA. Depending on the force and the molecules used, both smooth
elastic behaviors and abrupt structural transitions are observed. Third, we
show how combining the elasticity of two single nucleic acid strands with a
description of the base-pairing interactions between them explains much of the
phenomenology and kinetics of RNA and DNA `unzipping' experiments. | null |
|
2004-04-01T00:00:00 | A Molecular Matter-Wave Amplifier | Chris P. Search, Pierre Meystre | We describe a matter-wave amplifier for vibrational ground state molecules,
which uses a Feshbach resonance to first form quasi-bound molecules starting
from an atomic Bose-Einstein condensate. The quasi-bound molecules are then
driven into their stable vibrational ground state via a two-photon Raman
transition inside an optical cavity. The transition from the quasi-bound state
to the electronically excited state is driven by a classical field.
Amplification of ground state molecules is then achieved by using a strongly
damped cavity mode for the transition from the electronically excited molecules
to the molecular ground state. | 10.1103/PhysRevLett.93.140405 |
|
2004-09-06T00:00:00 | Mechanically-adjustable and electrically-gated single-molecule transistors | A. R. Champagne, A. N. Pasupathy, D. C. Ralph | We demonstrate a device geometry for single-molecule electronics experiments
that combines both the ability to adjust the spacing between the electrodes
mechanically and the ability to shift the energy levels in the molecule using a
gate electrode. With the independent in-situ variations of molecular properties
provided by these two experimental "knobs", we are able to achieve a much more
detailed characterization of electron transport through the molecule than is
possible with either technique separately. We illustrate the devices'
performance using C60 molecules. | 10.1021/nl0480619 |
|
2004-12-22T00:00:00 | Interactions between the Molecules of Different Fullerenes | V. I. Zubov | Generalizing the procedures of Girifalco and of Verheijen et al. and using
results of the preceding work it has been derived the interaction potential
between the molecules of different fullerenes Cn and Cm at orientationally
disordered (high-temperature solid and gaseous) phases. We have calculated the
coefficients for interactions of the C60 molecule with the molecules of higher
fullerenes from C70 to C96 and with the smaller one, C36. The dependence of the
minimum point and of the depth of the potential well on the numbers of the
atoms in the molecules m and n has been investigated. | Fullerenes, Nanotubes, and Carbon Nanostructures12 (2004) 499 -
504 | null |
2005-05-30T00:00:00 | Atom-molecule dark states in a Bose-Einstein condensate | K. Winkler, G. Thalhammer, M. Theis, H. Ritsch, R. Grimm, J. Hecker Denschlag | We have created a dark quantum superposition state of a Rb Bose-Einstein
condensate (BEC) and a degenerate gas of Rb$_2$ ground state molecules in a
specific ro-vibrational state using two-color photoassociation. As a signature
for the decoupling of this coherent atom-molecule gas from the light field we
observe a striking suppression of photoassociation loss. In our experiment the
maximal molecule population in the dark state is limited to about 100 Rb$_2$
molecules due to laser induced decay. The experimental findings can be well
described by a simple three mode model. | PRL 95, 063202 (2005) | 10.1103/PhysRevLett.95.063202 |
2005-06-14T00:00:00 | Dynamical projection of atoms to Feshbach molecules at strong coupling | R. A. Barankov, L. S. Levitov | The dynamical atom/molecule projection, recently used to probe fermion
pairing, is fast compared to collective fermion times, but slow on the Feshbach
resonance width scale. Theory of detuning-induced dynamics of molecules coupled
to resonantly associating atom pairs, employing a time-dependent many-body
Green's function approach, is presented. An exact solution is found, predicting
a 1/3 power law for molecule production efficiency at fast sweep. The results
for $s$- and p-wave resonances are obtained and compared. The predicted
production efficiency agrees with experimental observations for both condensed
and incoherent molecules away from saturation. | null |
|
2005-06-30T00:00:00 | Current-carrying molecules: a real space picture | Anna Painelli | An approach is presented to calculate characteristic current vs voltage
curves for isolated molecules without explicit description of leads. The
Hamiltonian for current-carrying molecules is defined by making resort to
Lagrange multipliers, while the potential drop needed to sustain the current is
calculated from the dissipated electrical work. Continuity constraints for
steady-state DC current result in non-linear potential profiles across the
molecule leading, in the adopted real-space picture, to a suggestive analogy
between the molecule and an electrical circuit. | null |
|
2005-10-13T00:00:00 | Control of topography, stress and diffusion at molecule-metal interface | Nikolai B. Zhitenev, Weirong Jiang, Artur Erbe, Zhenan Bao, Eric Garfunkel, Donald M. Tennant, Raymond A. Cirelli | Transport properties of metal-molecule-metal junctions containing monolayer
of conjugated and saturated molecules with characteristic dimensions in the
range of 30-300 nm are correlated with microscopic topography, stress and
chemical bonding at metal-molecule interfaces. Our statistically significant
dataset allows us to conclude that the conductivity of organic molecules ~1.5
nm long is at least 4 orders of magnitude lower than is commonly believed. | 10.1088/0957-4484/17/5/019 |
|
2007-03-03T00:00:00 | p-wave Feshbach molecules | J. P. Gaebler, J. T. Stewart, J. L. Bohn, D. S. Jin | We have produced and detected molecules using a p-wave Feshbach resonance
between 40K atoms. We have measured the binding energy and lifetime for these
molecules and we find that the binding energy scales approximately linearly
with magnetic field near the resonance. The lifetime of bound p-wave molecules
is measured to be 1.0 +/- 0.1 ms and 2.3 +/- 0.2 ms for the m_l = +/- 1 and m_l
= 0 angular momentum projections, respectively. At magnetic fields above the
resonance, we detect quasi-bound molecules whose lifetime is set by the
tunneling rate through the centrifugal barrier. | Phys. Rev. Lett. 98, 200403 (2007) | 10.1103/PhysRevLett.98.200403 |
2000-08-07T00:00:00 | Inelastic Collisions of Ultracold Polar Molecules | John L. Bohn | The collisional stability of ultracold polar molecules in electrostatic traps
is considered. Rate constants for collisions that drive molecules from
weak-field-seeking to strong-field-seeking states are estimated using a simple
model. The rates are found to be quite large, of order 10^{-12} - 10^{-10}
cm^3/sec, and moreover to grow rapidly in an externally applied electric field.
It is argued that these results are generic for polar molecules, and that
therefore polar molecules should be trapped by other than electrostatic means. | 10.1103/PhysRevA.63.052714 |
|
2000-08-30T00:00:00 | Transitions Induced by the Discreteness of Molecules in a Small Autocatalytic System | Yuichi Togashi, Kunihiko Kaneko | Autocatalytic reaction system with a small number of molecules is studied
numerically by stochastic particle simulations. A novel state due to
fluctuation and discreteness in molecular numbers is found, characterized as
extinction of molecule species alternately in the autocatalytic reaction loop.
Phase transition to this state with the change of the system size and flow is
studied, while a single-molecule switch of the molecule distributions is
reported. Relevance of the results to intracellular processes are briefly
discussed. | Phys. Rev. Lett. 86, 2459 (2001) | 10.1103/PhysRevLett.86.2459 |
2003-02-12T00:00:00 | Variational Analysis for Photonic Molecules | Bin-Shei Lin | A new type of artificial molecule is proposed, which consists of coupled
defect atoms in photonic crystals, named as photonic molecule. Within the major
band gap, the photonic molecule confines the resonant modes that are closely
analogous to the ground states of molecular orbitals. By employing the
variational theory, the constraint determining the resonant coupling is
formulated, that is consistent with the results of both the scattering method
and the group analysis. In addition, a new type of photonic waveguide is
proposed that manipulates the mechanism of photon hopping between photonic
molecules and offers a new optical feature of twin waveguiding bandwidths. | null |
|
2005-09-18T00:00:00 | Bi-Analyte Surface Enhanced Raman Scattering for unambiguous evidence of single molecule detection | E. C. Le Ru, M. Meyer, P. G. Etchegoin | A method is proposed to pin down an unambiguous proof for single molecule
surface enhanced Raman spectroscopy (SERS). The simultaneous use of two analyte
molecules enables a clear confirmation of the single (or few) molecule nature
of the signals. This method eliminates most of the uncertainties associated
with low dye concentrations in previous experiments. It further shows that
single-molecule signals are very common in SERS, both in liquids and on dry
substrates. | null |
|
2006-06-02T00:00:00 | Controlling electronic spin relaxation of cold molecules with electric fields | T. V. Tscherbul, R. V. Krems | We present a theoretical study of atom - molecule collisions in superimposed
electric and magnetic fields and show that dynamics of electronic spin
relaxation in molecules at temperatures below 0.5 K can be manipulated by
varying the strength and the relative orientation of the applied fields. The
mechanism of electric field control of Zeeman transitions is based on an
intricate interplay between intramolecular spin-rotation couplings and
molecule-field interactions. We suggest that electric fields may affect
chemical reactions through inducing nonadiabatic spin transitions and
facilitate evaporative cooling of molecules in a magnetic trap. | Phys. Rev. Lett. 97, 083201 (2006) | 10.1103/PhysRevLett.97.083201 |
2003-01-18T00:00:00 | Geometric Phase of electrons due to the Spin-rotation Coupling in Rotating C$_{60}$ Molecules | Jian-Qi Shen, Shao Long He | The rapidly rotational motion of C$_{60}$ molecules provides us with an
ingenious way to test Mashhoon's spin-rotation coupling. The spin-rotation
coupling of electrons in the rotating C$_{60}$ molecule is considered in the
present letter. It is shown that the intrinsic spin (gravitomagnetic moment) of
the electron that can be coupled to the time-dependent rotating frequency of
rotating frame of reference (C$_{60}$ molecule) results in a geometric phase,
which may be measured through the electronic energy spectra of C$_{60}$
molecules. | Phys. Rev. B 68, 195421 (2003) | 10.1103/PhysRevB.68.195421 |
2006-11-09T00:00:00 | Ab-initio path integral techniques for molecules | Daejin Shin, Ming-Chak Ho, J. Shumway | Path integral Monte Carlo with Green's function analysis allows the sampling
of quantum mechanical properties of molecules at finite temperature. While a
high-precision computation of the energy of the Born-Oppenheimer surface from
path integral Monte Carlo is quite costly, we can extract many properties
without explicitly calculating the electronic energies. We demonstrate how
physically relevant quantities, such as bond-length, vibrational spectra, and
polarizabilities of molecules may be sampled directly from the path integral
simulation using Matsubura (temperature) Green's functions (imaginary-time
correlation functions). These calculations on the hydrogen molecule are a
proof-of-concept, designed to motivate new work on fixed-node path-integral
calculations for molecules. | null |
|
2007-08-02T00:00:00 | Fast recognition of single molecules based on single event photon statistics | Shuangli Dong, Tao Huang, Yuan Liu, Jun Wang, Guofeng Zhang, Liantuan Xiao+, Suotang Jia | Mandel Q-parameter, which is determined from single event photon statistics,
provides an alternative to differentiate single-molecule with fluorescence
detection. In this work, by using the Q-parameter of the sample fluorescence
compared to that of an ideal double-molecule system with the same average
photon number, we present a novel and fast approach for identifying single
molecules based on single event photon statistics analyses, compared with
commonly used two-time correlation measurements. The error estimates for
critical values of photon statistics are also presented for single-molecule
determination. | 10.1103/PhysRevA.76.063820 |
|
2008-07-12T00:00:00 | Electronic structures of organic molecule encapsulated BN nanotubes under transverse electric field | Wei He, Zhenyu Li, Jinlong Yang, J. G. Hou | The electronic structures of boron nitride nanotubes (BNNTs) doped by
different organic molecules under a transverse electric field were investigated
via first-principles calculations. The external field reduces the energy gap of
BNNT, thus makes the molecular bands closer to the BNNT band edges and enhances
the charge transfers between BNNT and molecules. The effects of the electric
field direction on the band structure are negligible. The electric field
shielding effect of BNNT to the inside organic molecules is discussed. Organic
molecule doping strongly modifies the optical property of BNNT, and the
absorption edge is red-shifted under static transverse electric field. | J. Chem. Phys. 129, 024710 (2008) | 10.1063/1.2946708 |
2008-08-05T00:00:00 | Molecules in Coorbit Spaces and Boundedness of Operators | Karlheinz Gröchenig Mariusz Piotrowski | We study the notion of molecules in coorbit spaces. The main result states
that if an operator, originally defined on an appropriate space of test
functions, maps atoms to molecules, then it can be extended to a bounded
operator on coorbit spaces. For time-frequency molecules we recover some
boundedness results on modulation spaces, for time-scale molecules we obtain
the boundedness on homogenous Besov spaces. | Studia Math. 192(1) (2009), 61 - 77 | null |
2008-10-08T00:00:00 | Electron Transfer from Hydrogen Molecule to Au(111) During Dissociative Adsorption: A First-Principles Study | Shigeyuki Takagi, Jun-ichi Hoshino, Hidekazu Tomono, Kazuo Tsumuraya | We investigate the electron transfer from a dissociatively adsorbed H2
molecule to a Au(111) surface using the first-principles methods. A fractional
electron transfers from a molecule to a substrate, and potential energy
increases during the process. The initial energy increase coincides with that
of the isolated, separated, and positively charged H2 molecule calculated by
the real-space density functional method. The barrier formation is due to the
destabilization of the molecule induced by the electron transfer. The
electronegativity difference between the adsorbate and the substrate determines
the direction of the electron transfer. | J. Phys. Soc. Jpn. 77 (2008) 054705 | 10.1143/JPSJ.77.054705 |
2008-11-18T00:00:00 | Giant thermopower and figure of merit in single-molecule devices | C. M. Finch, V. M. García-Suárez, C. J. Lambert | We present a study of the thermopower $S$ and the dimensionless figure of
merit $ZT$ in molecules sandwiched between gold electrodes. We show that for
molecules with side groups, the shape of the transmission coefficient can be
dramatically modified by Fano resonances near the Fermi energy, which can be
tuned to produce huge increases in $S$ and $ZT$. This shows that molecules
exhibiting Fano resonances have a high efficiency of thermoelectric cooling
which is not present for conventional un-gated molecules with only delocalized
states along their backbone. | 10.1103/PhysRevB.79.033405 |
|
2009-01-24T00:00:00 | Ultracold molecules: new probes on the variation of fundamental constants | Cheng Chin, V. V. Flambaum, M. G. Kozlov | Ultracold molecules offer brand new opportunities to probe the variation of
fundamental constants with unprecedented sensitivity. This paper summarizes
theoretical background and current constraints on the variation of fine
structure constant and electron-to-proton mass ratio, as well as proposals and
experimental efforts to measure the variations based on ultracold molecules. In
particular, we describe two novel spectroscopic schemes on ultracold molecules
which have greatly enhanced sensitivity to fundamental constants: resonant
scattering near Feshbach resonances and spectroscopy on close-lying energy
levels of ultracold molecules. | New Journal of Physics 11 055048 (2009) | 10.1088/1367-2630/11/5/055048 |
2009-04-01T00:00:00 | Far-field Super-resolution Imaging with Dual-Dye-Doped Nanoparticles | Jianfang Chen, Ya Cheng | We propose to achieve super-resolution in far-field imaging by use of
dual-dye-doped nanoparticles. The nanoparticles with a diameter of a few
nanometers are co-doped with two types of dye molecules, namely, Cy3 and Cy5,
at a controllable ratio. Due to the short distances between the dye molecules
confined in the nanoparticles, Forster resonant energy transfer can occur
between the Cy3 and Cy5 molecules with high efficiency. Therefore, the Cy5
molecules can quench the fluorescence emission from the Cy3 molecules in the
outer region of focal spot of the excitation beam, thereby enhancing the
resolution of imaging. | 10.1364/OL.34.001831 |
|
2009-06-22T00:00:00 | Investigation of the interaction of some astrobiological molecules with the surface of a graphite (0001) substrate. Application to the CO, HCN, H2O and H2CO molecules | Azzedine Lakhlifi, John P. Killingbeck | Detailed semi-empirical interaction potential calculations are performed to
determine the potential energy surface experienced by the molecules CO, HCN,
H2O and H2CO, when adsorbed on the basal plane (0001) of graphite at low
temperature. The potential energy surface is used to find the equilibrium site
and configuration of a molecule on the surface and its corresponding adsorption
energy. The diffusion constant associated with molecular surface diffusion is
calculated for each molecule. | 10.1016/j.susc.2009.10.017 |
|
2010-02-04T00:00:00 | Near-infrared single-photons from aligned molecules in ultrathin crystalline films at room temperature | C. Toninelli, K. Early, J. Bremi, A. Renn, S. Goetzinger, V. Sandoghdar | We investigate the optical properties of Dibenzoterrylene (DBT) molecules in
a spin-coated crystalline film of anthracence. By performing single molecule
studies, we show that the dipole moments of the DBT molecules are oriented
parallel to the plane of the film. Despite a film thickness of only 20 nm, we
observe an exceptional photostability at room temperature and photon count
rates around one million per second from a single molecule. These properties
together with an emission wavelength around 800 nm make this system attractive
for applications in nanophotonics and quantum optics. | 10.1364/OE.18.006577 |
|
2010-06-16T00:00:00 | Microwave Lens for Polar Molecules | Hitoshi Odashima, Simon Merz, Katsunari Enomoto, Melanie Schnell, Gerard Meijer | We here report on the implementation of a microwave lens for neutral polar
molecules suitable to focus molecules both in low-field-seeking and in
high-field-seeking states. By using the TE_11m modes of a 12 cm long
cylindrically symmetric microwave resonator, Stark-decelerated ammonia
molecules are transversally confined. We investigate the focusing properties of
this microwave lens as a function of the molecules' velocity, the detuning of
the microwave frequency from the molecular resonance frequency, and the
microwave power. Such a microwave lens can be seen as a first important step
towards further microwave devices, such as decelerators and traps. | Phys. Rev. Lett. 104, 253001 (2010) | 10.1103/PhysRevLett.104.253001 |
2011-03-29T00:00:00 | An electrostatic elliptical mirror for neutral polar molecules | A. Isabel González Flórez, Samuel A. Meek, Henrik Haak, Horst Conrad, Gabriele Santambrogio, Gerard Meijer | Focusing optics for neutral molecules finds application in shaping and
steering molecular beams. Here we present an electrostatic elliptical mirror
for polar molecules consisting of an array of microstructured gold electrodes
deposited on a glass substrate. Alternating positive and negative voltages
applied to the electrodes create a repulsive potential for molecules in
low-field-seeking states. The equipotential lines are parallel to the substrate
surface, which is bent in an elliptical shape. The mirror is characterized by
focusing a beam of metastable CO molecules and the results are compared to the
outcome of trajectory simulations. | 10.1039/C1CP20957D |
|
2011-03-30T00:00:00 | Controlling the phase of a light beam with a single molecule | M. Pototschnig, Y. Chassagneux, J. Hwang, G. Zumofen, A. Renn, V. Sandoghdar | We employ heterodyne interferometry to investigate the effect of a single
organic molecule on the phase of a propagating laser beam. We report on the
first phase-contrast images of individual molecules and demonstrate a
single-molecule electro-optical phase switch by applying a voltage to the
microelectrodes embedded in the sample. Our results may find applications in
single-molecule holography, fast optical coherent signal processing, and
single-emitter quantum operations. | 10.1103/PhysRevLett.107.063001 |
|
2011-07-20T00:00:00 | Stern-Gerlach deflection of field-free aligned paramagnetic molecules | E. Gershnabel, M. Shapiro, I. Sh. Averbukh | The effects of laser-induced prealignment on the deflection of paramagnetic
molecules by inhomogeneous static magnetic field are studied. Depending on the
relevant Hund's coupling case of the molecule, two different effects were
identified: either suppression of the deflection by laser pulses (Hund's
coupling case (a) molecules, such as ClO), or a dramatic reconstruction of the
broad distribution of the scattering angles into several narrow peaks (for
Hund's coupling case (b) molecules, such as O2 or NH). These findings are
important for various applications using molecular guiding, focusing and
trapping with the help of magnetic fields. | 10.1063/1.3662135 |
|
2012-02-03T00:00:00 | Efficient method for quantum calculations of molecule - molecule scattering properties in a magnetic field | Y. V. Suleimanov, T. V. Tscherbul, R. V. Krems | We show that the cross sections for molecule - molecule collisions in the
presence of an external field can be computed efficiently using a total angular
momentum basis, defined either in the body-fixed frame or in the space-fixed
coordinate system. This method allows for computations with much larger basis
sets than previously possible. We present calculations for 15NH - 15NH
collisions in a magnetic field. Our results support the conclusion of the
previous study that the evaporative cooling of rotationally ground 15NH
molecules in a magnetic trap has a prospect of success. | J. Chem. Phys. 137, 024103 (2012) | 10.1063/1.4733288 |
2012-11-08T00:00:00 | Rovibrational cooling of molecules by optical pumping | I. Manai, R. Horchani, H. Lignier, A. Fioretti, M. Allegrini, P. Pillet, D. Comparat | We demonstrate rotational and vibrational cooling of cesium dimers by optical
pumping techniques. We use two laser sources exciting all the populated
rovibrational states, except a target state that thus behaves like a dark state
where molecules pile up thanks to absorption-spontaneous emission cycles. We
are able to accumulate photoassociated cold Cs2 molecules in their absolute
ground state (v = 0, J = 0) with up to 40% efficiency. Given its simplicity,
the method could be extended to other molecules and molecular beams. It also
opens up general perspectives in laser cooling the external degrees of freedom
of molecules. | Phys. Rev. Lett. 109, 183001 (2012) | 10.1103/PhysRevLett.109.183001 |
2012-11-18T00:00:00 | Modifying molecular scattering from rough solid surfaces using ultrashort laser pulses | Yuri Khodorkovsky, J. R. Manson, Ilya Sh. Averbukh | We consider solid surface scattering of molecules that were subject to strong
non-resonant ultrashort laser pulses just before hitting the surface. The
pulses modify the rotational states of the molecules, causing their field free
alignment, or a rotation with a preferred sense. We show that field-free
laser-induced molecular alignment leads to correlations between the scattering
angle and the sense of rotation of the scattered molecules. Moreover, by
controlling the sense of laser induced unidirectional molecular rotation, one
may affect the scattering angle of the molecules. This provides a new means for
separation of mixtures of molecules (such as isotopes and nuclear-spin isomers)
by laser controlled surface scattering. | 10.1080/00268976.2013.776710 |
|
2013-01-20T00:00:00 | Quantum Effects at Low Energy Atom-Molecule Interface | B. Deb, A. Rakshit, J. Hazra, D. Chakraborty | Quantum interference effects in inter-conversion between cold atoms and
diatomic molecules are analysed. Within the framework of Fano's theory,
continuum-bound anisotropic dressed state formalism of atom-molecule quantum
dynamics is presented. This formalism is applicable in photo- and
magneto-associative strong-coupling regimes. The significance of Fano effect in
ultracold atom-molecule transitions is discussed. Quantum effects at low energy
atom-molecule interface are important for exploring coherent phenomena in
hither-to unexplored parameter regimes. | Pramana - journal of physics, January 2013, Volume 80, Issue 1, pp
3-19 | 10.1007/s12043-012-0473-4 |
2013-02-12T00:00:00 | Van der Waals coefficients for systems with ultracold polar alkali-metal molecules | P. S. Zuchowski, M. Kosicki, M. Kodrycka, P. Soldan | A systematic study of the leading isotropic van der Waals coefficients for
the alkali-metal atom + molecule and molecule + molecule systems is presented.
Dipole moments and static and dynamic dipole polarizabilities are calculated
employing high-level quantum chemistry calculations. The dispersion, induction,
and rotational parts of the isotropic van der Waals coefficient are evaluated.
The known van der Waals coefficients are then used to derive characteristics
essential for simple models of the collisions involving the corresponding
ultracold polar molecules. | Phys. Rev. A 87, 022706 (2013) | 10.1103/PhysRevA.87.022706 |
2013-03-18T00:00:00 | Combinatorial expressions of the solutions to initial value problems of the discrete and ultradiscrete Toda molecules | Shuhei Kamioka, Tomoaki Takagaki | Combinatorial expressions are presented to the solutions to initial value
problems of the discrete and ultradiscrete Toda molecules. For the discrete
Toda molecule, a subtraction-free expression of the solution is derived in
terms of non-intersecting paths, for which two results in combinatorics,
Flajolet's interpretation of continued fractions and Gessel--Viennot's lemma on
determinants, are applied. By ultradiscretizing the subtraction-free
expression, the solution to the ultradiscrete Toda molecule is obtained. It is
finally shown that the initial value problem of the ultradiscrete Toda molecule
is exactly solved in terms of shortest paths on a specific graph. | 10.1088/1751-8113/46/35/355203 |
|
2013-03-25T00:00:00 | Optical Activity and Mirror-Symmetry | Won-Young Hwang | A misconception that non-chiral molecules have no optical activity at all is
widespread. However, at molecular level even non-chiral molecules have optical
activity. Optical activity of a non-chiral molecule is canceled out by that of
another molecule in its mirror image in normal liquids. We describe the
canceling mechanism by using mirror-symmetry of physical laws without resorting
to detailed formulas. The description will be helpful for overcoming the
misconception. Optical activity can be understood from the opposite viewpoint
by the description. Aligned non-chiral molecules have optical activity. | null |
|
2014-09-13T00:00:00 | Intermolecular Casimir-Polder Forces in Water and near Surfaces | Priyadarshini Thiyam, Clas Persson, Bo E. Sernelius, Drew F. Parsons, Anders Malthe-Sørenssen, Mathias Boström | The Casimir-Polder force is an important long range interaction involved in
adsorption and desorption of molecules in fluids. We explore Casimir-Polder
interactions between methane molecules in water, and between a molecule in
water near SiO2 and hexane surfaces. Inclusion of the finite molecular size in
the expression for the Casimir-Polder energy leads to estimates of the
dispersion contribution to the binding energies between molecules and between
one molecule and a planar surface. | Phys. Rev. E 90, 032122 (2014) | 10.1103/PhysRevE.90.032122 |
2015-09-12T00:00:00 | Trapping molecules on chips | Gabriele Santambrogio | In the last years, it was demonstrated that neutral molecules can be loaded
on a microchip directly from a supersonic beam. The molecules are confined in
microscopic traps that can be moved smoothly over the surface of the chip. Once
the molecules are trapped, they can be decelerated to a standstill, for
instance, or pumped into selected quantum states by laser light or microwaves.
Molecules are detected on the chip by time-resolved spatial imaging, which
allows for the study of the distribution in the phase space of the molecular
ensemble. | EPJ Techniques and Instrumentation, 2, 14 (2015) | 10.1140/epjti/s40485-015-0024-8 |
2017-06-29T00:00:00 | The sign of the polarizability anisotropy of polar molecules is obtained faithfully from terahertz Kerr effect | Tobias Kampfrath, Martin Wolf, Mohsen Sajadi | Optically heterodyned detected terahertz Kerr effect of gases of polar
molecules is reported. Strikingly, the birefringence signal from fluoroform is
found to have opposite polarity compared to water and acetonitrile. This
behavior is a hallmark of the opposite sign of the polarizability anisotropy of
these molecules. Resonant excitation of the rotational degrees of freedom of
the molecules aligns their permanent dipoles along the terahertz electric
field. This alignment is translated into an optical birefringence through the
polarizability anisotropy of each molecule. Therefore, the resulting net signal
scales with the polarizability anisotropy, whose sign is imprinted faithfully
onto the transient birefringence signal. | 10.1016/j.cplett.2017.12.061 |
|
2014-02-03T00:00:00 | Magnetism and Magnetic Anisotropy of Transition Metal-Phthalocyanine Molecules | Jun Hu, Ruqian Wu | Search for single-molecule magnets (SMMs) with high blocking temperature (TB)
is urgent for practical applications in magnetic recording, molecular
spintronics and quantum computing. Based on the First-principles calculations,
magnetic anisotropy energies (MAE) of the transition metal-Phthalocyanine
(TM-Pc) molecules are investigated and the mechanism that determines the MAE of
TM-Pc molecules is established. In particular, colossal MAE > 100 meV can be
obtained by adding an Os atom on RuPc and OsPc, so these molecules may offer
ultrahigh thermal stability in devices. | null |
|
2018-06-18T00:00:00 | Orientation-dependent hyperfine structure of polar molecules in a rare-gas matrix: a scheme for measuring the electron electric dipole moment | A. C. Vutha, M. Horbatsch, E. A. Hessels | Because molecules can have their orientation locked when embedded into a
solid rare-gas matrix, their hyperfine structure is strongly perturbed relative
to the freely rotating molecule. The addition of an electric field further
perturbs the structure, and fields parallel and antiparallel to the molecular
orientation result in different shifts of the hyperfine structure. These shifts
enable the selective detection of molecules with different orientations
relative to the axes of a rare-gas crystal, which will be an important
ingredient of an improved electron electric dipole moment measurement using
large ensembles of polar molecules trapped in rare-gas matrices. | Phys. Rev. A 98, 032513 (2018) | 10.1103/PhysRevA.98.032513 |
2018-06-23T00:00:00 | Dynamics of Single Molecule Stokes Shifts: Influence of Conformation and Environment | Martin Streiter, Stefan Krause, Christian von Borczyskowski, Carsten Deibel | We report on time dependent Stokes shift measurements of single molecules.
Broadband excitation and emission spectroscopy were applied to study the
temporal Stokes shift evolution of single perylene diimide molecules (PDI)
embedded in a polymer matrix on the time scale of seconds. The Stokes shift
varied between individual molecules as well as for single molecules undergoing
different conformations and geometries. From the distribution and temporal
evolution of Stokes shifts, we unravel the interplay of nano-environment and
molecular conformation. We found that Stokes shift fluctuations are related to
simultaneous and unidirectional shifts of both emission and excitation spectra. | The Journal of Physical Chemistry Letters 2016 7 (21), 4281-4284 | 10.1021/acs.jpclett.6b02102 |
2019-02-14T00:00:00 | Laser cooling of molecules | M. R. Tarbutt | Recently, laser cooling methods have been extended from atoms to molecules.
The complex rotational and vibrational energy level structure of molecules
makes laser cooling difficult, but these difficulties have been overcome and
molecules have now been cooled to a few microkelvin and trapped for several
seconds. This opens many possibilities for applications in quantum science and
technology, controlled chemistry, and tests of fundamental physics. This
article explains how molecules can be decelerated, cooled and trapped using
laser light, reviews the progress made in recent years, and outlines some
future applications. | 10.1080/00107514.2018.1576338 |
|
2019-02-27T00:00:00 | DFT study of five-membered ring PAHs | Gauri Devi, Mridusmita Buragohain, Amit Pathak | This work reports a 'Density Functional Theory' (DFT) calculation of PAH
molecules with a five-member ring to determine the expected region of infrared
features. It is highly possible that fullerene molecule might be originated
from five-membered ring PAH molecules in the ISM. Effect of ionization and
protonation on five-membered ring PAH molecule is also discussed. A detail
vibrational analysis of five-membered ring PAH molecule has been reported to
further compare with observations and to identify any observational
counterpart. | 10.1016/j.pss.2018.09.003 |
|
2010-08-23T00:00:00 | Distinguishing left- and right-handed molecules by two-step coherent pulses | W. Z. Jia, L. F. Wei | Chiral molecules with broken parity symmetries can be modeled as quantum
systems with cyclic-transition structures. By using these novel properties, we
design two-step laser pulses to distinguish left- and right-handed molecules
from the enantiomers. After the applied pulse drivings, one kind chiral
molecules are trapped in coherent population trapping state, while the other
ones are pumped to the highest states for ionizations. Then, different chiral
molecules can be separated. | 10.1088/0953-4075/43/18/185402 |
|
2010-08-30T00:00:00 | Coherent transfer of photoassociated molecules into the rovibrational ground state | K. Aikawa, D. Akamatsu, M. Hayashi, K. Oasa, J. Kobayashi, P. Naidon, T. Kishimoto, M. Ueda, S. Inouye | We report on the direct conversion of laser-cooled 41K and 87Rb atoms into
ultracold 41K87Rb molecules in the rovibrational ground state via
photoassociation followed by stimulated Raman adiabatic passage.
High-resolution spectroscopy based on the coherent transfer revealed the
hyperfine structure of weakly bound molecules in an unexplored region. Our
results show that a rovibrationally pure sample of ultracold ground-state
molecules is achieved via the all-optical association of laser-cooled atoms,
opening possibilities to coherently manipulate a wide variety of molecules. | 10.1103/PhysRevLett.105.203001 |
|
2016-07-23T00:00:00 | Electrodynamical Forbiddance of the Strong Quadrupole Light-Molecule Interaction and Its Experimental Manifestation in Fullerene C60 | V. P. Chelibanov, A. M. Polubotko | It is demonstrated that the forbidden lines, which must be present in the
SERS, TERS and SEIRA spectra of molecules with sufficiently high symmetry,
associated with a strong quadrupole light-molecule interaction, are absent in
the fullerene C60. This result is an experimental manifestation of an
electrodynamical forbiddance of the strong quadrupole light-molecule
interaction, which must be not only in molecules with cubic symmetry groups,
but in the fullerene C60 also. | 10.1016/j.cplett.2016.10.034 |
|
2017-11-26T00:00:00 | Hyperfine structure of 2Sigma molecules containing alkaline-earth atoms | Jesus Aldegunde, Jeremy M. Hutson | Ultracold molecules with both electron spin and an electric dipole moment
offer new possibilities in quantum science. We use density-functional theory to
calculate hyperfine coupling constants for a selection of molecules important
in this area, including RbSr, LiYb, RbYb, CaF and SrF. We find substantial
hyperfine coupling constants for the fermionic isotopes of the alkaline-earth
and Yb atoms. We discuss the hyperfine level patterns and Zeeman splittings
expected for these molecules. The results will be important both to experiments
aimed at forming ultracold open-shell molecules and to their applications. | Phys. Rev. A 97, 042505 (2018) | 10.1103/PhysRevA.97.042505 |
2018-09-13T00:00:00 | Front-propagation in bacterial inter-colony communication | Vera Bettenworth, Matthew McIntosh, Anke Becker, Bruno Eckhardt | Many bacterial species exchange signaling molecules to coordinate
population-wide responses. For this process known as quorum sensing the
concentration of the respective molecules is crucial. Here we consider the
interaction between spatially distributed bacterial colonies so that the
spreading of the signaling molecules in space becomes important. The
exponential growth of the signal-producing populations and the corresponding
increase in signaling molecule production result in an exponential
concentration profile that spreads with uniform speed. The theoretical
predictions are supported by experiments with different strains of the soil
bacterium Sinorhizobium meliloti that display fluorescence when either
producing or responding to the signaling molecules. | 10.1063/1.5040068 |
|
2010-11-14T00:00:00 | Mechanical control of vibrational states in single-molecule junctions | Youngsang Kim, Hyunwook Song, Florian Strigl, Hans-Fridtjof Pernau, Takhee Lee, Elke Scheer | We report on inelastic electron tunneling spectroscopy measurements carried
out on single molecules incorporated into a mechanically controllable
break-junction of Au and Pt electrodes at low temperature. Here we establish a
correlation between the molecular conformation and conduction properties of a
single-molecule junction. We demonstrate that the conductance through single
molecules crucially depends on the contact material and configuration by virtue
of their mechanical and electrical properties. Our findings prove that the
charge transport via single molecules can be manipulated by varying both the
molecular conformation (e.g., trans or gauche) and the contact material. | null |
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