-
Direct Time-Domain Observation of l-Doubling via Centrifugal-Distortion Pre-compensation
Authors:
Inbar Sternbach,
Kfir Rutman Moshe,
Amit Beer,
Soumitra Hazra,
Sharly Fleischer
Abstract:
We demonstrate direct time-domain observation of l-doubling contributions in molecular rotational dynamics using shaped femtosecond laser pulses. By imposing a tailored spectral phase on the excitation pulse, we pre-compensate centrifugal distortion, which otherwise leads to temporally broadened, multi-cycle revival structures that obscure fine rotational features. A cubic spectral phase [Phys. Re…
▽ More
We demonstrate direct time-domain observation of l-doubling contributions in molecular rotational dynamics using shaped femtosecond laser pulses. By imposing a tailored spectral phase on the excitation pulse, we pre-compensate centrifugal distortion, which otherwise leads to temporally broadened, multi-cycle revival structures that obscure fine rotational features. A cubic spectral phase [Phys. Rev. A 107, 053108 (2023)] compresses selected revivals into near single-cycle events, in agreement with an analytic expression derived from molecular rotational constants, enabling predictive pulse design beyond numerical optimization. The resulting distortion-free revivals reveal temporally separated l-doubling contributions that remain unresolved in conventional impulsive alignment experiments. The method proves robust against experimental imperfections, including spatial light modulator discretization. While selective control of individual l-doubling components becomes feasible, here we focus on their direct observation in the time domain.
△ Less
Submitted 4 May, 2026;
originally announced May 2026.
-
Irreversibility and symmetry breaking in the creation and annihilation of defects in active living matter
Authors:
Avraham Beer,
Efraim Dov Neimand,
Yuv Agarwal,
Dom Corbett,
Daniel J. G. Pearce,
Gil Ariel,
Victor Yashunsky
Abstract:
Active living matter continuously creates and annihilates topological defects in a process that remains poorly understood. Here, we investigate these dynamics in two distinct active living systems: swarming bacteria and human bronchial epithelial cells. Despite their entirely different evolutionary origins, biological functions, and physical scales, both systems exhibit half-integer defects, consi…
▽ More
Active living matter continuously creates and annihilates topological defects in a process that remains poorly understood. Here, we investigate these dynamics in two distinct active living systems: swarming bacteria and human bronchial epithelial cells. Despite their entirely different evolutionary origins, biological functions, and physical scales, both systems exhibit half-integer defects, consistent with the nematic phase. However, in contrast to active nematic theory, we find that defect creation and annihilation undergoes spatial symmetry breaking. We propose that these results stem from a fundamental dualism between nematic structural organization and generated polar forces, which are intrinsic to living systems. Furthermore, estimation of entropy production reveals that creation and annihilation are not reversed processes. Our findings challenge conventional nematic models and emphasize the role of defect-mediated dynamics in non-equilibrium biological systems as a major source of entropy production.
△ Less
Submitted 4 March, 2026; v1 submitted 21 August, 2025;
originally announced August 2025.
-
Immobility of isolated swarmer cells due to local liquid depletion
Authors:
Ajesh Jose,
Benjamin Perez-Estay,
Shira Omer Bendori,
Avigdor Eldar,
Daniel B. Kearns,
Gil Ariel,
Avraham Beer
Abstract:
Bacterial swarming is a complex phenomenon in which thousands of self-propelled rod-shaped cells move coherently on surfaces, providing an excellent example of active matter. However, bacterial swarming is different from most studied examples of active systems because single isolated cells do not move, while clusters do. The biophysical aspects underlying this behavior are unclear. In this work we…
▽ More
Bacterial swarming is a complex phenomenon in which thousands of self-propelled rod-shaped cells move coherently on surfaces, providing an excellent example of active matter. However, bacterial swarming is different from most studied examples of active systems because single isolated cells do not move, while clusters do. The biophysical aspects underlying this behavior are unclear. In this work we explore the case of low local cell densities, where single cells become temporarily immobile. We show that immobility is related to local depletion of liquid. In addition, it is also associated with the state of the flagella. Specifically, the flagellar bundles at (temporarily) liquid depleted regions are completely spread-out. Our results suggest that dry models of self-propelled agents, which only consider steric alignments and neglect hydrodynamic effects, are oversimplified and are not sufficient to describe swarming bacteria.
△ Less
Submitted 26 November, 2024;
originally announced November 2024.
-
Temporal Subspace Clustering for Molecular Dynamics Data
Authors:
Anna Beer,
Martin Heinrigs,
Claudia Plant,
Ira Assent
Abstract:
We introduce MOSCITO (MOlecular Dynamics Subspace Clustering with Temporal Observance), a subspace clustering for molecular dynamics data. MOSCITO groups those timesteps of a molecular dynamics trajectory together into clusters in which the molecule has similar conformations. In contrast to state-of-the-art methods, MOSCITO takes advantage of sequential relationships found in time series data. Unl…
▽ More
We introduce MOSCITO (MOlecular Dynamics Subspace Clustering with Temporal Observance), a subspace clustering for molecular dynamics data. MOSCITO groups those timesteps of a molecular dynamics trajectory together into clusters in which the molecule has similar conformations. In contrast to state-of-the-art methods, MOSCITO takes advantage of sequential relationships found in time series data. Unlike existing work, MOSCITO does not need a two-step procedure with tedious post-processing, but directly models essential properties of the data. Interpreting clusters as Markov states allows us to evaluate the clustering performance based on the resulting Markov state models. In experiments on 60 trajectories and 4 different proteins, we show that the performance of MOSCITO achieves state-of-the-art performance in a novel single-step method. Moreover, by modeling temporal aspects, MOSCITO obtains better segmentation of trajectories, especially for small numbers of clusters.
△ Less
Submitted 31 July, 2024;
originally announced August 2024.
-
Enhanced molecular orientation via NIR-delay-THz scheme: Experimental results at room temperature
Authors:
Ran Damari,
Amit Beer,
Eli Flaxer,
Sharly Fleischer
Abstract:
THz fields induce orientation in gas phase molecules via resonant dipole-field interaction. The degree of orientation however remains severely limited due to the practical shortage of high THz-field amplitudes. In this paper, we experimentally demonstrate a concerted Near-IR and THz excitation scheme that provides significant increase in the degree of orientation at room temperature gas ensembles.…
▽ More
THz fields induce orientation in gas phase molecules via resonant dipole-field interaction. The degree of orientation however remains severely limited due to the practical shortage of high THz-field amplitudes. In this paper, we experimentally demonstrate a concerted Near-IR and THz excitation scheme that provides significant increase in the degree of orientation at room temperature gas ensembles. The experimental results are supported by theoretical simulations and a detailed discussion of the multiple coherent transition pathways involved in the scheme is presented.
△ Less
Submitted 29 October, 2022;
originally announced October 2022.
-
Orientation Echoes via Concerted Terahertz and Near-IR excitation
Authors:
Ran Damari,
Amit Beer,
Sharly Fleischer
Abstract:
A new and efficient method for orientation echo spectroscopy is presented and realized experimentally. The excitation scheme utilizes concerted rotational excitations by both ultrashort terahertz and near-IR pulses and its all-optical detection is enabled by Molecular Orientation Induced Second Harmonic method [J.Phys.Chem.A 126, 3732-3738 (2022)]. The method provides practical means for orientati…
▽ More
A new and efficient method for orientation echo spectroscopy is presented and realized experimentally. The excitation scheme utilizes concerted rotational excitations by both ultrashort terahertz and near-IR pulses and its all-optical detection is enabled by Molecular Orientation Induced Second Harmonic method [J.Phys.Chem.A 126, 3732-3738 (2022)]. The method provides practical means for orientation echo spectroscopy of gas phase molecules and highlights the intriguing underlying physics of coherent rotational dynamics induced by judiciously-orchestrated interactions with both resonant (terahertz) and nonresonant (NIR) light pulses.
△ Less
Submitted 3 August, 2022;
originally announced August 2022.
-
Molecular Orientation-Induced Second Harmonic Generation: deciphering different contributions apart
Authors:
Amit Beer,
Ran Damari,
Yun Chen,
Sharly Fleischer
Abstract:
We demonstrate and explore an all-optical technique for direct monitoring the orientation dynamics of gas phase molecular ensembles. The technique termed 'MOISH' utilizes the transiently lifted inversion symmetry of polar gas media and provides a sensitive and spatially localized probing of second harmonic generation signal that is directly correlated with the orientation of the gas. Our experimen…
▽ More
We demonstrate and explore an all-optical technique for direct monitoring the orientation dynamics of gas phase molecular ensembles. The technique termed 'MOISH' utilizes the transiently lifted inversion symmetry of polar gas media and provides a sensitive and spatially localized probing of second harmonic generation signal that is directly correlated with the orientation of the gas. Our experimental results reveal selective electronic and nuclear dynamical contributions to the overall nonlinear optical signal and decipher them apart using the "reporter gas" approach. 'MOISH' provides new, crucial means for exploring controlled rotational dynamics via concerted terahertz and optical field excitation.
△ Less
Submitted 7 March, 2022;
originally announced March 2022.
-
A phase diagram for bacterial swarming
Authors:
Avraham Be`er,
Bella Ilkanaiv,
Renan Gross,
Daniel B. Kearns,
Sebastian Heidenreich,
Markus Bär,
Gil Ariel
Abstract:
Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize a surface. Physically, swarming is a natural example of active particles that use energy to generate motion. Accordingly, understanding the constraints physics imposes on the dynamics is essential to understand the mechanisms underlying the swarming phenomenon. We present new experiments of sw…
▽ More
Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize a surface. Physically, swarming is a natural example of active particles that use energy to generate motion. Accordingly, understanding the constraints physics imposes on the dynamics is essential to understand the mechanisms underlying the swarming phenomenon. We present new experiments of swarming Bacillus subtilis mutants with different aspect ratios and densities. Analyzing the dynamics reveals a rich phase diagram of qualitatively distinct swarming regimes, describing how the shape and density of cells govern the global dynamical characteristics of the entire swarm. Moreover, we show that under standard conditions bacteria inhabit a region of phase space that is associated with rapid mixing and robust dynamics, with homogeneous density and no preferred direction of motion. This contrasts characteristic clustering behavior of self-propelled rods that is recovered only for very elongated mutant species. Thus, bacteria have adapted their physics to optimize the principle functions assumed for swarming.
△ Less
Submitted 13 November, 2019;
originally announced November 2019.
-
Iris-assisted Terahertz Field-Induced Second Harmonic Generation in Air
Authors:
Amit Beer,
Dror Hershkovitz,
Sharly Fleischer
Abstract:
Terahertz field-induced second harmonic generation (TFISH) is a technique for optical detection of broad-band THz fields. We show that by placing an iris at the interaction volume of the THz and optical fields, the TFISH signal increases by few ten-fold in atmospheric air. The iris-assisted TFISH amplification is characterized at varying air pressures and probe intensities and provides an elegant…
▽ More
Terahertz field-induced second harmonic generation (TFISH) is a technique for optical detection of broad-band THz fields. We show that by placing an iris at the interaction volume of the THz and optical fields, the TFISH signal increases by few ten-fold in atmospheric air. The iris-assisted TFISH amplification is characterized at varying air pressures and probe intensities and provides an elegant platform for studying nonlinear phase-matching in the gas phase.
△ Less
Submitted 24 June, 2019;
originally announced June 2019.
-
Enhancement of muonium emission rate from silica aerogel with a laser ablated surface
Authors:
G. A. Beer,
Y. Fujiwara,
S. Hirota,
K. Ishida,
M. Iwasaki,
S. Kanda,
H. Kawai,
N. Kawamura,
R. Kitamura,
S. Lee,
W. Lee G. M. Marshall,
T. Mibe,
Y. Miyake,
S. Okada,
K. Olchanski,
A. Olin,
Y. Oishi,
H. Onishi,
M. Otani,
N. Saito,
K. Shimomura,
P. Strasser,
M. Tabata,
D. Tomono,
K. Ueno
, et al. (2 additional authors not shown)
Abstract:
Emission of muonium ($μ^+e^-$) atoms from a laser-processed aerogel surface into vacuum was studied for the first time. Laser ablation was used to create hole-like regions with diameter of about 270$~μ$m in a triangular pattern with hole separation in the range of 300--500$~μ$m. The emission probability for the laser-processed aerogel sample is at least eight times higher than for a uniform one.
Emission of muonium ($μ^+e^-$) atoms from a laser-processed aerogel surface into vacuum was studied for the first time. Laser ablation was used to create hole-like regions with diameter of about 270$~μ$m in a triangular pattern with hole separation in the range of 300--500$~μ$m. The emission probability for the laser-processed aerogel sample is at least eight times higher than for a uniform one.
△ Less
Submitted 30 July, 2014;
originally announced July 2014.
-
Measurement of muonium emission from silica aerogel
Authors:
P. Bakule,
G. A. Beer,
D. Contreras,
M. Esashi,
Y. Fujiwara,
Y. Fukao,
S. Hirota,
H. Iinuma,
K. Ishida,
M. Iwasaki,
T. Kakurai,
S. Kanda,
H. Kawai,
N. Kawamura,
G. M. Marshall,
H. Masuda,
Y. Matsuda,
T. Mibe,
Y. Miyake,
S. Okada,
K. Olchanski,
A. Olin,
H. Onishi,
N. Saito,
K. Shimomura
, et al. (6 additional authors not shown)
Abstract:
Emission of muonium ($μ^{+}e^{-}$) atoms from silica aerogel into vacuum was observed. Characteristics of muonium emission were established from silica aerogel samples with densities in the range from 29 mg cm$^{-3}$ to 178 mg cm$^{-3}$. Spectra of muonium decay times correlated with distances from the aerogel surfaces, which are sensitive to the speed distributions, follow general features expect…
▽ More
Emission of muonium ($μ^{+}e^{-}$) atoms from silica aerogel into vacuum was observed. Characteristics of muonium emission were established from silica aerogel samples with densities in the range from 29 mg cm$^{-3}$ to 178 mg cm$^{-3}$. Spectra of muonium decay times correlated with distances from the aerogel surfaces, which are sensitive to the speed distributions, follow general features expected from a diffusion process, while small deviations from a simple room-temperature thermal diffusion model are identified. The parameters of the diffusion process are deduced from the observed yields.
△ Less
Submitted 17 June, 2013;
originally announced June 2013.
-
Label-free, Spectroscopic Detection of Leaflet Composition Asymmetry in Vesicles
Authors:
Matthew L. Strader,
Hilton Barbosa de Aguiar,
Alex G. F. de Beer,
Sylvie Roke
Abstract:
Vibrational sum frequency scattering (SFS) has been used to study sub-micron, catanionic vesicles in solution. The vesicles were synthesized from a binary mixture of dodecyltrimethylammonium bromide (DTAB) and sodium dodecylsulfate (SDS) surfactants in deuterated water, which spontaneously assemble into thermodynamically stable vesicles. The stability of these vesicles is attributed to a surfactan…
▽ More
Vibrational sum frequency scattering (SFS) has been used to study sub-micron, catanionic vesicles in solution. The vesicles were synthesized from a binary mixture of dodecyltrimethylammonium bromide (DTAB) and sodium dodecylsulfate (SDS) surfactants in deuterated water, which spontaneously assemble into thermodynamically stable vesicles. The stability of these vesicles is attributed to a surfactant concentration asymmetry between the inner and outer bilayer leaflets. This concentration asymmetry should be observable by SFS due to local inversion symmetry-breaking. Signal corresponding to the symmetric sulfate stretch mode of the SDS head group is observed at 1044 cm, indicating that there is indeed asymmetry in the local structure of the leaflets. The results indicate that it should be possible to measure the interfacial structure of liposomes in aqueous solution and study in-situ processes like the binding of sugars and proteins that are important for many processes in biophysical chemistry.
△ Less
Submitted 30 November, 2010; v1 submitted 23 May, 2010;
originally announced May 2010.
-
Resonant Scattering of Muonic Hydrogen Atoms and Dynamics of Muonic Molecular Complex
Authors:
TRIUMF Munoic Hydrogen Collaboration,
M. C. Fujiwara,
A. Adamczak,
J. M. Bailey,
G. A. Beer,
J. L. Beveridge,
M. P. Faifman,
T. M. Huber,
P. Kammel,
S. K. Kim,
P. E. Knowles,
A. R. Kunselman,
M. Maier,
V. E. Markushin,
G. M. Marshall,
C. J. Martoff,
G. R. Mason,
F. Mulhauser,
A. Olin,
C. Petitjean,
T. A. Porcelli,
J. Wozniak,
J. Zmeskal
Abstract:
Resonant scattering of muonic hydrogen atoms via back decay of molecular complex, a key process in the understanding of epithermal muonic molecular formation, is analyzed. The limitations of the effective rate approximation are discussed and the importance of the explicit treatment of the back decay is stressed. An expression of the energy distribution for the back-decayed atoms is given.
Resonant scattering of muonic hydrogen atoms via back decay of molecular complex, a key process in the understanding of epithermal muonic molecular formation, is analyzed. The limitations of the effective rate approximation are discussed and the importance of the explicit treatment of the back decay is stressed. An expression of the energy distribution for the back-decayed atoms is given.
△ Less
Submitted 29 November, 2001;
originally announced November 2001.
-
Measurement of the Resonant $dμt$ Molecular Formation Rate in Solid HD
Authors:
T. A. Porcelli,
A. Adamczak,
J. M. Bailey,
G. A. Beer,
J. L. Douglas,
M. P. Faifman,
M. C. Fujiwara,
T. M. Huber,
P. Kammel,
S. K. Kim,
P. E. Knowles,
A. R. Kunselman,
M. Maier,
V. E. Mar kushin,
G. M. Marshall,
G. R. Mason,
F. Mulhauser,
A. Olin,
C. Petitjean,
J. Zmeskal
Abstract:
Measurements of muon-catalyzed dt fusion ($dμt \to ^4He+n+μ^-$) in solid HD have been performed. The theory describing the energy dependent resonant molecular formation rate for the reaction $μt$ + HD $\to [(dμt)pee]^*$ is compared to experimental results in a pure solid HD target. Constraints on the rates are inferred through the use of a Monte Carlo model developed specifically for the experim…
▽ More
Measurements of muon-catalyzed dt fusion ($dμt \to ^4He+n+μ^-$) in solid HD have been performed. The theory describing the energy dependent resonant molecular formation rate for the reaction $μt$ + HD $\to [(dμt)pee]^*$ is compared to experimental results in a pure solid HD target. Constraints on the rates are inferred through the use of a Monte Carlo model developed specifically for the experiment. From the time-of- flight analysis of fusion events in 16 and 37 $μg\cdot cm^{-2}$ targets, an average formation rate consistent with 0.897$\pm$(0.046)$_{stat}\pm$ (0.166)$_{syst}$ times the theoretical prediction was obtained.
△ Less
Submitted 2 April, 2001;
originally announced April 2001.
-
Time-of-Flight Spectroscopy of Muonic Hydrogen Atoms and Molecules
Authors:
TRIUMF Muonic Hydrogen Collaboration,
M. C. Fujiwara,
A. Adamczak,
J. M. Bailey,
G. A. Beer,
J. L. Beveridge,
M. P. Faifman,
T. M. Huber,
P. Kammel,
S. K. Kim,
P. E. Knowles,
A. R. Kunselman,
V. E. Markushin,
G. M. Marshall,
G. R. Mason,
F. Mulhauser,
A. Olin,
C. Petitjean,
T. A. Porcelli,
J. Zmeskal
Abstract:
Studies of muonic hydrogen atoms and molecules have been performed traditionally in bulk targets of gas, liquid or solid. At TRIUMF, Canada's meson facility, we have developed a new type of target system using multilayer thin films of solid hydrogen, which provides a beam of muonic hydrogen atoms in vacuum. Using the time-of-flight of the muonic atoms, the energy-dependent information of muonic…
▽ More
Studies of muonic hydrogen atoms and molecules have been performed traditionally in bulk targets of gas, liquid or solid. At TRIUMF, Canada's meson facility, we have developed a new type of target system using multilayer thin films of solid hydrogen, which provides a beam of muonic hydrogen atoms in vacuum. Using the time-of-flight of the muonic atoms, the energy-dependent information of muonic reactions are obtained in direct manner. We discuss some unique measurements enabled by the new technique, with emphasis on processes relevant to muon catalyzed fusion.
△ Less
Submitted 22 January, 2001;
originally announced January 2001.
-
Using Thin Film Targets for Muonic Atoms and Muon Catalyzed Fusion Studies
Authors:
TRIUMF Munoic Hydrogen Collaboration,
M. C. Fujiwara,
A. Adamczak,
J. M. Bailey,
G. A. Beer,
J. L. Beveridge,
M. P. Faifman,
T. M. Huber,
P. Kammel,
S. K. Kim,
P. E. Knowles,
A. R. Kunselman,
V. E. Markushin,
G. M. Marshall,
C. J. Martoff,
G. R. Mason,
F. Mulhauser,
A. Olin,
C. Petitjean,
T. A. Porcelli,
J. Zmeskal
Abstract:
Studies of muonic atoms and muon catalyzed fusion have been conventionally done in a bulk target of gas, liquid or solid hydrogen isotopes. The use of thin film targets developed at TRIUMF have notable advantages in tackling some of the most important questions in the field, which could be further exploited at future high intensity muon sources. We review the technique of the thin film method wi…
▽ More
Studies of muonic atoms and muon catalyzed fusion have been conventionally done in a bulk target of gas, liquid or solid hydrogen isotopes. The use of thin film targets developed at TRIUMF have notable advantages in tackling some of the most important questions in the field, which could be further exploited at future high intensity muon sources. We review the technique of the thin film method with emphasis on recent results and a future proposal.
△ Less
Submitted 3 September, 2000;
originally announced September 2000.
-
Resonant Formation of $dμt$ Molecules in Deuterium: An Atomic Beam Measurement of Muon Catalyzed dt Fusion
Authors:
TRIUMF Munoic Hydrogen Collaboration,
M. C. Fujiwara,
A. Adamczak,
J. M. Bailey,
G. A. Beer,
J. L. Beveridge,
M. P. Faifman,
T. M. Huber,
P. Kammel,
S. K. Kim,
P. E. Knowles,
A. R. Kunselman,
M. Maier,
V. E. Markushin,
G. M. Marshall,
C. J. Martoff,
G. R. Mason,
F. Mulhauser,
A. Olin,
C. Petitjean,
T. A. Porcelli,
J. Wozniak,
J. Zmeskal
Abstract:
Resonant formation of $dμt$ molecules in collisions of muonic tritium ($μt$) on D$_2$ was investigated using a beam of $μt$ atoms, demonstrating a new direct approach in muon catalyzed fusion studies. Strong epithermal resonances in $dμt$ formation were directly revealed for the first time. From the time-of-flight analysis of $2036\pm 116$ $dt$ fusion events, a formation rate consistent with…
▽ More
Resonant formation of $dμt$ molecules in collisions of muonic tritium ($μt$) on D$_2$ was investigated using a beam of $μt$ atoms, demonstrating a new direct approach in muon catalyzed fusion studies. Strong epithermal resonances in $dμt$ formation were directly revealed for the first time. From the time-of-flight analysis of $2036\pm 116$ $dt$ fusion events, a formation rate consistent with $0.73\pm (0.16)_{meas} \pm (0.09)_{model}$ times the theoretical prediction was obtained. For the largest peak at a resonance energy of $0.423 \pm 0.037$ eV, this corresponds to a rate of $(7.1 \pm 1.8) \times 10^9$ s$^{-1}$, more than an order of magnitude larger than those at low energies.
△ Less
Submitted 6 August, 2000;
originally announced August 2000.