Showing 1–50 of 66 results for author: Qiu, T

A Perspective on Phase Space Electronic Structure Theory : From Its Surface Hopping Origins Through To Its Future Promise

Authors: Joseph E. Subotnik, Ethan Alguire, Nicole Bellonzi, Xuezhi Bian, Mansi Bhati, Nadine Bradbury, D. Vale Cofer-Shabica, Ben Curlee, Titouan Duston, Shervin Fatehi, Gaohan Miao, Zheng Pei, Linqing Peng, Tian Qiu, Zhen Tao, Hung-Hsuan Teh, Xinchun Wu, Yanze Wu, Zain Zaidi, Yihan Shao, Jonathan Rawlinson, Neil Shenvi, Robert Littlejohn

Abstract: We trace the history of phase space electronic structure theory (PSEST), high- lighting how this powerful approach emerged from fundamental questions in semi- classical surface hopping dynamics and evolved into an alternative to standard Born- Oppenheimer based electronic structure theory (with moving instead of frozen nuclei). Our goal herein is not to recapitulate the mathematical details of pha… ▽ More We trace the history of phase space electronic structure theory (PSEST), high- lighting how this powerful approach emerged from fundamental questions in semi- classical surface hopping dynamics and evolved into an alternative to standard Born- Oppenheimer based electronic structure theory (with moving instead of frozen nuclei). Our goal herein is not to recapitulate the mathematical details of phase space electronic structure calculations, and few equations are presented so as to maximize readability. Instead, our goal is to provide intuition for those new to the field both (i) regarding the physics present when solving the Schrodinger equation in a non-inertial frame as well as (ii) regarding why PSEST is a necessary step forward towards understanding chemical problems involving spin (with limited practical alternatives). We further high- light some of the many open questions in this fast developing area, which will hopefully inspire new practitioners in this field. This intuitive perspective lacks many equations and is meant to complement (rather than replace) the more technical review given in Bian et al, Chem. Phys. Rev. 7, 011303 (2026) △ Less

Submitted 15 August, 2026; v1 submitted 11 August, 2026; originally announced August 2026.

Simulation of complex DNA damage enhancement and biological effect validation for Proton-CAT

Authors: Lang Dong, Dechao An, Junxiang Wu, Tianle Wang, Zhao Sun, Jiajun Kang, Xianliang Wang, Lintao Li, Shun Lu, Tianli Qiu, Da Zhang, Zhencen He, Zhimin Hu

Abstract: Proton therapy has been rapidly advancing due to its excellent conformal index, but its relatively low relative biological effect (RBE) has somewhat limited its therapeutic efficacy for certain tumors. To address this, we previously proposed a nitrogen-targeting Proton-Carbon-Alpha-Therapy (Proton-CAT) enhancement method. In this letter, we present combined multi-scale DNA damage simulations and i… ▽ More Proton therapy has been rapidly advancing due to its excellent conformal index, but its relatively low relative biological effect (RBE) has somewhat limited its therapeutic efficacy for certain tumors. To address this, we previously proposed a nitrogen-targeting Proton-Carbon-Alpha-Therapy (Proton-CAT) enhancement method. In this letter, we present combined multi-scale DNA damage simulations and in vitro cell experiments, further investigating the mechanism of the Proton-CAT. It has been show that $^{15}$N enrichment significantly enhances complex DNA damage induced by high linear energy transfer(LET) particles within tumor regions. Under 30\% $^{15}$N conditions, $α$ and $^{12}$C particle induced DSB++ increased by 175.19\% and 52.94\%, respectively. Furthermore, in vitro cell experiments using $^{15}$N-glutamine ($^{15}$N-Glu) as the $^{15}$N carrier indicated that high concentrations of $^{15}$N-Glu did not bring about significant cytotoxicity. Following 2 Gy irradiation, the cell viability in the 500 $μ$g/mL $^{15}$N-Glu treated group exhibited a net reduction of about 15.41\% compared to the control group.This indicates that the enhanced effect of Proton-CAT primarily stems from increased complex DNA damage. This work provides a theoretical basis and multi-scale research framework for the development of the Proton-CAT. △ Less

Submitted 29 April, 2026; originally announced April 2026.

Comments: 5 pages, 5 figures

Charge Transfer with a Spin. II: A Framework for Diabatization which Localizes Charge and Spin

Authors: Alok Kumar, Zhen Tao, Zuxin Jin, Joseph E. Subotnik, Tian Qiu

Abstract: We investigate a diabatization procedure that localizes charges (in real space) and localizes spins (in spin space) for open-shell systems that exhibit charge transfer in the presence of spin-orbit coupling. The procedure is applied to a two-state crossing between pairs of Kramers-restricted doublet states (which can also be considered effectively a four-state crossing). To generate the relevant e… ▽ More We investigate a diabatization procedure that localizes charges (in real space) and localizes spins (in spin space) for open-shell systems that exhibit charge transfer in the presence of spin-orbit coupling. The procedure is applied to a two-state crossing between pairs of Kramers-restricted doublet states (which can also be considered effectively a four-state crossing). To generate the relevant electronic states, we employ the recently developed electron/hole-transfer Dynamically-weighted State-Averaged Constrained CASSCF (eDSC/hDSC) method that treats systems with an odd number of electrons. To generate the relevant diabatic states, we employ a two-step optimization over complex-unitary rotations that sequentially maximizes dipole and spin moments through iterative Jacobi sweeps; the resulting update rules are effectively equivalent to those of approximate joint diagonalization (AJD) applied to charge and spin. The method converges rapidly and yields smooth diabatic potential energy surfaces that preserve dipole and spin properties (e.g., a slowly varying pseudospin texture) along the reaction coordinate while maintaining time-reversal symmetry. △ Less

Submitted 11 February, 2026; v1 submitted 7 February, 2026; originally announced February 2026.

Charge Transfer with a Spin. I: A Generalized CASSCF Framework for Investigating Charge Transfer in the Presence of Spin-Orbit Coupling

Authors: Alok Kumar, Zhen Tao, Joseph E. Subotnik, Tian Qiu

Abstract: We present a generalized extension of the recently developed electron/hole-transfer Dynamically-weighted State-Averaged Constrained CASSCF (eDSC/hDSC) method to model charge transfer in the presence of spin-orbit coupling (SOC) for systems containing an odd number of electrons. Our approach incorporates complex-valued spinor orbitals and incorporates four electronic configurations in describing gr… ▽ More We present a generalized extension of the recently developed electron/hole-transfer Dynamically-weighted State-Averaged Constrained CASSCF (eDSC/hDSC) method to model charge transfer in the presence of spin-orbit coupling (SOC) for systems containing an odd number of electrons. Our approach incorporates complex-valued spinor orbitals and incorporates four electronic configurations in describing ground-excited state curve crossings between Kramers-restricted doublet states. The method achieves smooth potential energy surfaces and rapid self-consistent field (SCF) convergence across a wide range of spin-orbit coupling strengths, providing an efficient framework for investigating charge transfer processes in the presence of nontrivial spin degrees of freedom. △ Less

Submitted 11 February, 2026; v1 submitted 7 February, 2026; originally announced February 2026.

Phase Space Electronic Structure Theory: From Diatomic Lambda-Doubling to Macroscopic Einstein-de Haas

Authors: Linqing Peng, Tian Qiu, Nadine Bradbury, Xuezhi Bian, Mansi Bhati, Robert Littlejohn, Nathanael M. Kidwell, Joseph E. Subotnik

Abstract: $Λ$-doubling of diatomic molecules is a subtle microscopic phenomenon that has long attracted the attention of experimental groups, insofar as rotation of molecular $\textit{nuclei}$ induces small energetic changes in the (degenerate) $\textit{electronic}… ▽ More $Λ$-doubling of diatomic molecules is a subtle microscopic phenomenon that has long attracted the attention of experimental groups, insofar as rotation of molecular $\textit{nuclei}$ induces small energetic changes in the (degenerate) $\textit{electronic}$ state. A direct description of such a phenomenon clearly requires going beyond the Born-Oppenheimer approximation. Here we show that a phase space theory previously developed to capture electronic momentum and model vibrational circular dichroism -- and which we have postulated should also describe the Einstein-de Haas effect, a macroscopic manifestation of angular momentum conservation -- is also able to recover the $Λ$-doubling energy splitting (or $Λ$-splitting) of the NO molecule nearly quantitatively. The key observation is that, by parameterizing the electronic Hamiltonian in terms of both nuclear position ($\mathbf{X}$) and nuclear momentum ($\mathbf{P}$), a phase space method yields potential energy surfaces that explicitly include the electron-rotation coupling and correctly conserve angular momentum (which we show is essential to capture $Λ-$doubling). The data presented in this manuscript offers another small glimpse into the rich physics that one can learn from investigating phase space potential energy surfaces $E_{PS}(\mathbf{X},\mathbf{P})$ as a function of both nuclear position and momentum, all at a computational cost comparable to standard Born-Oppenheimer electronic structure calculations. △ Less

Submitted 22 January, 2026; v1 submitted 15 December, 2025; originally announced December 2025.

Marcus Theory and The Condon Approximation Revisited II: The Horror of Triplet Energy Transfer

Authors: Jennifer R. DeRosa, Tian Qiu, D. Vale Cofer-Shabica, Joseph E. Subotnik

Abstract: We investigate the applicability of the Condon approximation (i.e. the notion that the diabatic coupling is invariant to geometry) in the context of both electron transfer (ET) and triplet energy transfer (TET) and compare the two cases. Although it is well appreciated that diabatic couplings usually arise from the interactions of electronic wavefunction tails, we show that ET tails are very diffe… ▽ More We investigate the applicability of the Condon approximation (i.e. the notion that the diabatic coupling is invariant to geometry) in the context of both electron transfer (ET) and triplet energy transfer (TET) and compare the two cases. Although it is well appreciated that diabatic couplings usually arise from the interactions of electronic wavefunction tails, we show that ET tails are very different from TET tails. Using a simple model problem, our analysis explains in detail why the rates of TET decays with twice the rate of ET, while also leading to the hypothesis that the smaller diabatic couplings found for TET (versus ET) should imply more sensitivity to non-Condon fluctuations. As an example, for the classic sets of molecules investigated by Closs, we show that the Condon approximation is indeed less applicable for TET than for ET. △ Less

Submitted 13 October, 2025; originally announced October 2025.

Comments: 32 pages, 9 figures, 1 TOC graphic

A Graph-Neural-Network-Entropy model of vital node identification on network attack and propagation

Authors: Huaizhi Liao, Tian Qiu, Guang Chen

Abstract: Vital nodes usually play a key role in complex networks. Uncovering these nodes is an important task in protecting the network, especially when the network suffers intentional attack. Many existing methods have not fully integrated the node feature, interaction and state. In this article, we propose a novel method (GNNE) based on graph neural networks and information entropy. The method employs a… ▽ More Vital nodes usually play a key role in complex networks. Uncovering these nodes is an important task in protecting the network, especially when the network suffers intentional attack. Many existing methods have not fully integrated the node feature, interaction and state. In this article, we propose a novel method (GNNE) based on graph neural networks and information entropy. The method employs a Graph Convolutional Network (GCN) to learn the nodes' features, which are input into a Graph Attention Network (GAT) to obtain the influence factor of nodes, and the node influence factors are used to calculate the nodes' entropy to evaluate the node importance. The GNNE takes advantage of the GCN and GAT, with the GCN well extracting the nodes' features and the GAT aggregating the features of the nodes' neighbors by using the attention mechanism to assign different weights to the neighbors with different importance, and the nodes' entropy quantifies the nodes' state in the network. The proposed method is trained on a synthetic Barabasi-Albert network, and tested on six real datasets. Compared with eight traditional topology-based methods and four graph-machine-learning-based methods, the GNNE shows an advantage for the vital node identification in the perspectives of network attack and propagation. △ Less

Submitted 22 September, 2025; originally announced September 2025.

Nonadiabatic H-Atom Scattering Channels on Ge(111) Elucidated by the Hierarchical Equations of Motion

Authors: Xiaohan Dan, Zhuoran Long, Tianyin Qiu, Jan Paul Menzel, Qiang Shi, Victor S. Batista

Abstract: Atomic and molecular scattering at semiconductor interfaces plays a central role in surface chemistry and catalysis, yet predictive simulations remain challenging due to strong nonadiabatic effects causing the breakdown of the Born-Oppenheimer approximation. Here, we present fully quantum simulations of H-atom scattering from the Ge(111)c(2x8) rest site using the hierarchical equations of motion (… ▽ More Atomic and molecular scattering at semiconductor interfaces plays a central role in surface chemistry and catalysis, yet predictive simulations remain challenging due to strong nonadiabatic effects causing the breakdown of the Born-Oppenheimer approximation. Here, we present fully quantum simulations of H-atom scattering from the Ge(111)c(2x8) rest site using the hierarchical equations of motion (HEOM) with matrix product states (MPS). The system is modeled by mapping a density functional theory (DFT) potential energy surface onto a Newns-Anderson Hamiltonian. Our simulations reproduce the experimentally observed bimodal kinetic energy distributions, capturing both elastic and energy-loss channels. By systematically examining atom-surface coupling, incident energy, and isotope substitution, we identify the strong-coupling regime required to recover the experimental energy-loss profile. This regime suppresses the elastic peak, implying additional site-specific scattering channels in the observed elastic peak. Deuterium substitution further produces a subtle shift in the energy-loss peak, consistent with experiment. These results establish HEOM as a rigorous framework for quantum surface scattering, capable of capturing nonadiabatic dynamics beyond electronic friction and perturbative approaches. △ Less

Submitted 14 January, 2026; v1 submitted 21 September, 2025; originally announced September 2025.

Journal ref: J. Chem. Phys. 164, 024115 (2026)

Fast Methods For Multisite Charge Transfer Processes II: Analytic Nuclear Gradients and Nonadiabatic Dynamics For cCASSCF(1,M) and cCASSCF(2M-1,M) Wavefunctions

Authors: Tian Qiu, Joseph E. Subotnik

Abstract: We derive and implement analytic nuclear gradients and derivative couplings for a constrained Complete Active Space Self-Consistent Field with a small active space designed to model electron or hole transfer. Using a Lagrangian formalism, we are able to differentiate both the CASSCF energy and the constraint (which is required for globally smooth surfaces), and the resulting efficient algorithm ca… ▽ More We derive and implement analytic nuclear gradients and derivative couplings for a constrained Complete Active Space Self-Consistent Field with a small active space designed to model electron or hole transfer. Using a Lagrangian formalism, we are able to differentiate both the CASSCF energy and the constraint (which is required for globally smooth surfaces), and the resulting efficient algorithm can be immediately applied to nonadiabatic dynamics simulations of charge transfer processes. Here, we run initial surface-hopping simulations of a proton coupled electron transfer event for a phenoxyl-phenol system. △ Less

Submitted 28 August, 2025; originally announced August 2025.

Fast Methods For Multisite Charge Transfer Processes I: Constrained, State Averaged CASSCF(1,M) and CASSCF(2M-1,M) Simulations

Authors: Tian Qiu, Joseph E. Subotnik

Abstract: We design a dynamically-weighted state-averaged constrained CASSCF to treat \ul{e}lectrons or \ul{h}oles moving between $n$ molecular fragments (where $n$ can be larger than 2). Within such a so-called eDSCn/hDSCn approach, we consider configurations that are mutually single excitations of each other, and we apply a generalized set of constraints to tailor the method for studying charge transfer p… ▽ More We design a dynamically-weighted state-averaged constrained CASSCF to treat \ul{e}lectrons or \ul{h}oles moving between $n$ molecular fragments (where $n$ can be larger than 2). Within such a so-called eDSCn/hDSCn approach, we consider configurations that are mutually single excitations of each other, and we apply a generalized set of constraints to tailor the method for studying charge transfer problems. The constrained optimization problem is efficiently solved using a DIIS-SQP algorithm, thus maintaining computational efficiency. We demonstrate the method for a finite Su-Schrieffer-Heeger (SSH) chain, successfully reproducing the expected exponential decay of diabatic couplings with distance. When combined with a gradient, the current extension immediately enables efficient nonadiabatic dynamics simulations of complex multi-state charge transfer processes. △ Less

Submitted 28 August, 2025; originally announced August 2025.

The Phase-Space Way To Electronic Structure Theory and Subsequently Chemical Dynamics

Authors: Xuezhi Bian, Titouan Duston, Nadine Bradbury, Zhen Tao, Mansi Bhati, Tian Qiu, Xinchun Wu, Yanze Wu, Joseph E. Subotnik

Abstract: Phase-space electronic structure theory offers up a new and powerful approach for tackling problems with coupled nuclear-electronic dynamics in a fashion that goes beyond Born-Oppenheimer (BO) theory. Whereas BO theory stipulates that we consider electronic states parameterized by nuclear position $X$ only, i.e. molecular orbitals are functions of nuclear positions but not nuclear velocities, phas… ▽ More Phase-space electronic structure theory offers up a new and powerful approach for tackling problems with coupled nuclear-electronic dynamics in a fashion that goes beyond Born-Oppenheimer (BO) theory. Whereas BO theory stipulates that we consider electronic states parameterized by nuclear position $X$ only, i.e. molecular orbitals are functions of nuclear positions but not nuclear velocities, phase-space (PS) theory allows for electronic states to be parameterized by both nuclear position X and nuclear momentum $P$. As a result, within a phase-space approach, one can directly recover many new features, including electronic momentum and vibrational circular dichroism spectra. Moreover, phase-space electronic structure theory is exact for the hydrogen atom and, for a set of model problems, the method can even improve upon vibrational energies relative to BO theory. Perhaps most importantly, the phase-space approach offers up a very new perspective on spin physics, stipulating that molecules and materials with degenerate or nearly degenerate ground states (due to spin degeneracy) display broken-symmetry ground states in their phase-space potential energy surfaces. This last feature opens up very new possibilities for exploring spin chemistry (including the Einstein-de Haas effect and chiral induced spin selectivity) within the context of more established electronic structure theory. At the end of the day, in order to tackle electronic dynamical phenomena, especially subtle problems in magnetic chemistry, it will be essential for the electronic structure community to pivot towards diagonalizing $\hat H_{PS}(X, P)$ rather than $\hat H_{BO}(X)$. △ Less

Submitted 28 July, 2025; v1 submitted 18 June, 2025; originally announced June 2025.

Dynamics of Spinning Test Body in quadratic Einstein-Cartan Theory and its Free-fall Test

Authors: Kun Hu, Zhiyuan Yu, Taotao Qiu, Zhongkun Hu

Abstract: We study the dynamics of the non-relativistic spinning test body (STB) in the framework of Einstein-Cartan theory(ECT), in which the weak equivalence principle is violated by the spin-gravitational interaction. We derive the general equation of geodesic in terms of comoving tetrads. More concretely, we consider the case of the quadratic form of the lagrangian, within the environment of weak and st… ▽ More We study the dynamics of the non-relativistic spinning test body (STB) in the framework of Einstein-Cartan theory(ECT), in which the weak equivalence principle is violated by the spin-gravitational interaction. We derive the general equation of geodesic in terms of comoving tetrads. More concretely, we consider the case of the quadratic form of the lagrangian, within the environment of weak and static spherically symmetric space-time. We find that the trajectories of STB deviate from the traditional Mathisson\textendash Papapetrou equation, which is due to the coupling of the spin of the test particle to the torsion field of the environment. This allows us to test the theory with free-fall experiment in the laboratory, such as atom interferometer. By using the previous data, we find the upper bound of the possible torsion field on Earth is given by up to $2.0\times 10^{1} \mathrm{~m^{-1}}$ and torsion gradient up to $3.1 \times 10^{-6}\mathrm{~m^{-2}}$. This result may enable us to provide a theoretical foundation for future precision measurements of the existence of the fifth force. △ Less

Submitted 31 March, 2025; originally announced March 2025.

Comments: 28 pages, 1 figure

Miniature magneto-oscillatory wireless sensor for magnetic field and gradient measurements

Authors: Felix Fischer, Moonkwang Jeong, Tian Qiu

Abstract: Magneto-oscillatory devices have been recently developed as very potent wireless miniature position trackers and sensors with an exceptional accuracy and sensing distance for surgical and robotic applications. However, it is still unclear to which extend a mechanically resonating sub-millimeter magnet interacts with external magnetic fields or gradients, which induce frequency shifts of sub-mHz to… ▽ More Magneto-oscillatory devices have been recently developed as very potent wireless miniature position trackers and sensors with an exceptional accuracy and sensing distance for surgical and robotic applications. However, it is still unclear to which extend a mechanically resonating sub-millimeter magnet interacts with external magnetic fields or gradients, which induce frequency shifts of sub-mHz to several Hz and therefore affect the sensing accuracy. Here, we investigate this effect experimentally on a cantilever-based magneto-oscillatory wireless sensor (MOWS) and build an analytical model concerning magnetic and mechanical interactions. The millimeter-scale MOWS is capable to detect magnetic fields with sub-uT resolution to at least +/- 5 mT, and simultaneously detects magnetic field gradients with a resolution of 65 uT/m to at least +/- 50 mT/m. The magnetic field sensitivity allows direct calculation of mechanical device properties, and by rotation, individual contributions of the magnetic field and gradient can be analyzed. The derived model is general and can be applied to other magneto-oscillatory systems interacting with magnetic environments. △ Less

Submitted 22 October, 2024; originally announced October 2024.

Comments: Main text: 7 pages with figures; Supplementary materials 6 pages with figures

Journal ref: Appl. Phys. Lett. 125, 074102 (2024)

Pockels Laser Directly Driving Ultrafast Optical Metrology

Authors: Shixin Xue, Mingxiao Li, Raymond Lopez-rios, Jingwei Ling, Zhengdong Gao, Qili Hu, Tian Qiu, Jeremy Staffa, Lin Chang, Heming Wang, Chao Xiang, John E. Bowers, Qiang Lin

Abstract: The invention of the laser unleashed the potential of optical metrology, leading to numerous advancements in modern science and technology. This reliance on lasers, however, also sets a bottleneck for precision optical metrology which is complicated by sophisticated photonic infrastructure required for delicate laser-wave control, leading to limited metrology performance and significant system com… ▽ More The invention of the laser unleashed the potential of optical metrology, leading to numerous advancements in modern science and technology. This reliance on lasers, however, also sets a bottleneck for precision optical metrology which is complicated by sophisticated photonic infrastructure required for delicate laser-wave control, leading to limited metrology performance and significant system complexity. Here we make a key step towards resolving this challenge, by demonstrating a Pockels laser with multi-functional capability that advances the optical metrology to a new level. The chip-scale laser exhibits a narrow intrinsic linewidth down to 167 Hz and a broad mode-hop-free tuning range up to 24 GHz. In particular, it offers an unprecedented frequency chirping rate up to 20 EHz/s, and an enormous modulation bandwidth >10 GHz, both orders of magnitude larger than any existing lasers. With this laser, we are able to successfully achieve velocimetry of 40 m/s at a short distance of 0.4 m, with a measurable velocity up to the first cosmic velocity at 1 m away, that is inaccessible by conventional ranging approaches, and distance metrology with a ranging resolution of <2 cm. Moreover, for the first time to the best of our knowledge, we are able to realize a dramatically simplified architecture for laser frequency stabilization, by direct locking the laser to an external reference gas cell without any extra external light control. We successfully achieve a long-term laser stability with a frequency fluctuation of only $\pm$ 6.5 MHz over 60 minutes. The demonstrated Pockels laser combines elegantly high laser coherence with ultrafast frequency reconfigurability and superior multifunctional capability that we envision to have profound impacts on many areas including communication, sensing, autonomous driving, quantum information processing, and beyond. △ Less

Submitted 9 October, 2024; originally announced October 2024.

Comments: 10 pages, 4 figures

A semiclassical non-adiabatic phase-space approach to molecular translations and rotations: A new picture of surface hopping and electronic inertial effects

Authors: Xuezhi Bian, Yanze Wu, Tian Qiu, Tao Zhen, Joseph E. Subotnik

Abstract: We present a novel semiclassical phase-space surface hopping approach that goes beyond the Born-Oppenheimer approximation and all existing surface hopping formalisms. We demonstrate that working with a correct phase-space electronic Hamiltonian can capture electronic inertial effects during pure nuclear translational and rotational motion and completely eliminate (at least to very high order) non-… ▽ More We present a novel semiclassical phase-space surface hopping approach that goes beyond the Born-Oppenheimer approximation and all existing surface hopping formalisms. We demonstrate that working with a correct phase-space electronic Hamiltonian can capture electronic inertial effects during pure nuclear translational and rotational motion and completely eliminate (at least to very high order) non-adiabatic transitions between electronic eigenstates. This work opens many new avenues for quantitatively investigating complex phenomena, including angular momentum transfer between chiral phonons and electrons as well as chiral-induced spin selectivity effects. △ Less

Submitted 1 October, 2024; originally announced October 2024.

An Efficient Algorithm for Constrained CASSCF(1,2) and CASSCF(3,2) Simulations as Relevant to Electron and Hole Transfer Problems

Authors: Tian Qiu, Joseph E. Subotnik

Abstract: We propose an efficient algorithm for the recently published electron/hole-transfer Dynamical-weighted State-averaged Constrained CASSCF (eDSC/hDSC) method studying charge transfer states and D$_1$-D$_0$ crossings for systems with odd numbers of electrons. By separating the constrained minimization problem into an unconstrained self-consistent-field (SCF) problem and a constrained non-self-consist… ▽ More We propose an efficient algorithm for the recently published electron/hole-transfer Dynamical-weighted State-averaged Constrained CASSCF (eDSC/hDSC) method studying charge transfer states and D$_1$-D$_0$ crossings for systems with odd numbers of electrons. By separating the constrained minimization problem into an unconstrained self-consistent-field (SCF) problem and a constrained non-self-consistent-field (nSCF) problem, and accelerating the direct inversion in the iterative subspace (DIIS) technique to solve the SCF problem, the overall computational cost is reduced by a factor of 8 to 20 compared with directly using sequential quadratic programming (SQP). This approach should be applicable for other constrained minimization problems and, in the immediate future, once gradients are available, the present eDSC/hDSC algorithm should allow for speedy non-adiabatic dynamics simulations. △ Less

Submitted 22 September, 2024; originally announced September 2024.

A Basis-Free Phase Space Electronic Hamiltonian That Recovers Beyond Born-Oppenheimer Electronic Momentum and Current Density

Authors: Zhen Tao, Tian Qiu, Xuezhi Bian, Joseph E. Subotnik

Abstract: We present a phase-space electronic Hamiltonian $\hat{H}_{PS}$ (parameterized by both nuclear position $\mathbf{X}$ and momentum $\mathbf{P}$) that boosts each electron into the moving frame of the nuclei that are closest in real space -- without presuming the existence of an atomic orbital basis. We show that $(i)$ quantum-classical dynamics along such a Hamiltonian maintains momentum conservatio… ▽ More We present a phase-space electronic Hamiltonian $\hat{H}_{PS}$ (parameterized by both nuclear position $\mathbf{X}$ and momentum $\mathbf{P}$) that boosts each electron into the moving frame of the nuclei that are closest in real space -- without presuming the existence of an atomic orbital basis. We show that $(i)$ quantum-classical dynamics along such a Hamiltonian maintains momentum conservation and $(ii)$ diagonalizing such a Hamiltonian can recover the electronic momentum and electronic current density reasonably well. In conjunction with other reports in the literature that such a phase-space approach can also recover vibrational circular dichroism (VCD) spectra, we submit that the present phase-space approach offers a testable and powerful approach to post-Born-Oppenheimer electronic structure theory. Moreover, the approach is inexpensive and can be immediately applied to simulations of chiral induced spin selectivity experiments (where the transfer of angular momentum between nuclei and electrons is considered critical). △ Less

Submitted 30 December, 2024; v1 submitted 23 July, 2024; originally announced July 2024.

Deep and Dynamic Metabolic and Structural Imaging in Living Tissues

Authors: Kunzan Liu, Honghao Cao, Kasey Shashaty, Li-Yu Yu, Sarah Spitz, Francesca Michela Pramotton, Zhengpeng Wan, Ellen L. Kan, Erin N. Tevonian, Manuel Levy, Eva Lendaro, Roger D. Kamm, Linda G. Griffith, Fan Wang, Tong Qiu, Sixian You

Abstract: Label-free imaging through two-photon autofluorescence (2PAF) of NAD(P)H allows for non-destructive and high-resolution visualization of cellular activities in living systems. However, its application to thick tissues and organoids has been restricted by its limited penetration depth within 300 $μ$m, largely due to tissue scattering at the typical excitation wavelength (~750 nm) required for NAD(P… ▽ More Label-free imaging through two-photon autofluorescence (2PAF) of NAD(P)H allows for non-destructive and high-resolution visualization of cellular activities in living systems. However, its application to thick tissues and organoids has been restricted by its limited penetration depth within 300 $μ$m, largely due to tissue scattering at the typical excitation wavelength (~750 nm) required for NAD(P)H. Here, we demonstrate that the imaging depth for NAD(P)H can be extended to over 700 $μ$m in living engineered human multicellular microtissues by adopting multimode fiber (MMF)-based low-repetition-rate high-peak-power three-photon (3P) excitation of NAD(P)H at 1100 nm. This is achieved by having over 0.5 MW peak power at the band of 1100$\pm$25 nm through adaptively modulating multimodal nonlinear pulse propagation with a compact fiber shaper. Moreover, the 8-fold increase in pulse energy at 1100 nm enables faster imaging of monocyte behaviors in the living multicellular models. These results represent a significant advance for deep and dynamic metabolic and structural imaging of intact living biosystems. The modular design (MMF with a slip-on fiber shaper) is anticipated to allow wide adoption of this methodology for demanding in vivo and in vitro imaging applications, including cancer research, autoimmune diseases, and tissue engineering. △ Less

Submitted 18 April, 2024; originally announced April 2024.

Comments: 20 pages, 5 figures, under review in Science Advances

A Miniaturized Device for Ultrafast On-demand Drug Release based on a Gigahertz Ultrasonic Resonator

Authors: Yangchao Zhou, Moonkwang Jeong, Meng Zhang, Xuexin Duan, Tian Qiu

Abstract: On-demand controlled drug delivery is essential for the treatment of a wide range of chronic diseases. As the drug is released at the time when required, its efficacy is boosted and the side effects are minimized. However, so far, drug delivery devices often rely on the passive diffusion process for a sustained release, which is slow and uncontrollable. Here, we present a miniaturized microfluidic… ▽ More On-demand controlled drug delivery is essential for the treatment of a wide range of chronic diseases. As the drug is released at the time when required, its efficacy is boosted and the side effects are minimized. However, so far, drug delivery devices often rely on the passive diffusion process for a sustained release, which is slow and uncontrollable. Here, we present a miniaturized microfluidic device for wirelessly controlled ultrafast active drug delivery, driven by an oscillating solid-liquid interface. The oscillation generates acoustic streaming in the drug reservoir, which opens an elastic valve to deliver the drug. High-speed microscopy reveals the fast response of the valve on the order of 1 ms, which is more than three orders of magnitude faster than the start-of-the-art. The amount of the released drug exhibits a linear relationship with the working time and the electric power applied to the ultrasonic resonator. The trigger of the release is wirelessly controlled via a magnetic field, and the system shows stable output in a continuous experiment for two weeks. The integrated system shows great promise as a long-term controlled drug delivery implant for chronic diseases. △ Less

Submitted 5 March, 2024; originally announced March 2024.

Comments: 19 pages, 6 figures, 1 table

MSC Class: J.3

Journal ref: \c{opyright} 2024 The Authors. Advanced Engineering Materials published by Wiley-VCH GmbH

Practical Phase-Space Electronic Hamiltonians for Ab Initio Dynamics

Authors: Zhen Tao, Tian Qiu, Mansi Bhati, Xuezhi Bian, Titouan Duston, Jonathan Rawlinson, Robert G. Littlejohn, Joseph E. Subotnik

Abstract: Modern electronic structure theory is built around the Born-Oppenheimer approximation and the construction of an electronic Hamiltonian H_{el}(X) that depends on the nuclear position X (and not the nuclear momentum P). In this article, using the well-known theory of electron translation (Gamma') and rotational (Gamma'') factors to couple electronic transitions to nuclear motion, we construct a pra… ▽ More Modern electronic structure theory is built around the Born-Oppenheimer approximation and the construction of an electronic Hamiltonian H_{el}(X) that depends on the nuclear position X (and not the nuclear momentum P). In this article, using the well-known theory of electron translation (Gamma') and rotational (Gamma'') factors to couple electronic transitions to nuclear motion, we construct a practical phase-space electronic Hamiltonian that depends on both nuclear position and momentum, H_{PS}(X,P). While classical Born-Oppenheimer dynamics that run along the eigensurfaces of the operator H_{el}(X) can recover many nuclear properties correctly, we present some evidence that motion along the eigensurfaces of H_{PS}(X,P) can better capture both nuclear and electronic properties (including the elusive electronic momentum studied by Nafie). Moreover, only the latter (as opposed to the former) conserves the total linear and angular momentum in general. △ Less

Submitted 30 January, 2024; v1 submitted 25 January, 2024; originally announced January 2024.

A Simple One-Electron Expression for Electron Rotational Factors

Authors: Tian Qiu, Mansi Bhati, Zhen Tao, Xuezhi Bian, Jonathan Rawlinson, Robert G. Littlejohn, Joseph E. Subotnik

Abstract: Within the context of FSSH dynamics, one often wishes to remove the angular component of the derivative coupling between states $\left|J\right>$ and $\left|K\right>$. In a set of previous papers, Truhlar {\em et al.} posited one approach for such a removal based on direct projection, while we isolated a second approach by constructing and differentiating rotationally invariant basis. Unfortunately… ▽ More Within the context of FSSH dynamics, one often wishes to remove the angular component of the derivative coupling between states $\left|J\right>$ and $\left|K\right>$. In a set of previous papers, Truhlar {\em et al.} posited one approach for such a removal based on direct projection, while we isolated a second approach by constructing and differentiating rotationally invariant basis. Unfortunately, neither approach was able to demonstrate a {\em one-electron operator} $\hat{O}$ whose matrix element $\left<J|\hat{O}|K\right>$ was the angular component of the derivative coupling. Here, we show that a one-electron operator can in fact be constructed efficiently in a semi-local fashion. The present results yield physical insight into designing new surface hopping algorithms and be of immediate use for FSSH calculations. △ Less

Submitted 24 January, 2024; originally announced January 2024.

Hydrogel modified evaporation interface for highly stable membrane distillation

Authors: Yanni Ma, Zehua Yu, Xifan Fu, Zhi Huang, Tenghui Qiu, Na Zhao, Huidong Liu, Kang Liu

Abstract: Surface effect of low-surface-tension contaminants accumulating at the evaporation surface can easily induce membrane wetting in the application of membrane distillation, especially in hypersaline scenarios. In this work, we propose a novel strategy to eliminate the surface effect and redistribute contaminants at the evaporation interface with simply incorporating a layer of hydrogel. The as-fabri… ▽ More Surface effect of low-surface-tension contaminants accumulating at the evaporation surface can easily induce membrane wetting in the application of membrane distillation, especially in hypersaline scenarios. In this work, we propose a novel strategy to eliminate the surface effect and redistribute contaminants at the evaporation interface with simply incorporating a layer of hydrogel. The as-fabricated composite membrane exhibits remarkable stability, even when exposed to extreme conditions, such as a salt concentration of 5M and surfactant concentration of 8 mM. The breakthrough pressure of the membrane is as high as 20 bars in the presence of surfactants, surpassing commercial hydrophobic membranes by one to two magnitudes. Combined study of density functional theory and molecular dynamics simulations reveals the important role of hydrogel-surfactant interaction in suppressing the surface effect. As a proof of concept, we also demonstrate the stable performance of the membrane in processing synthetic wastewater containing surfactants of 144 mg L-1, mineral oils of 1g L-1 and NaCl of 192 g L-1, showing potential of the membrane in addressing challenges of hypersaline water treatment and zero liquid discharge processes. △ Less

Submitted 5 December, 2023; originally announced December 2023.

Comments: 24 pages, 12 figures

STRAW-b (STRings for Absorption length in Water-b): the second pathfinder mission for the Pacific Ocean Neutrino Experiment

Authors: Kilian Holzapfel, Christian Spannfellner, Omid Aghaei, Andrew Baron, Jeanette Bedard, Michael Böhmer, Jeff Bosma, Nathan Deis, Christopher Fink, Christian Fruck, Andreas Gärtner, Roman Gernhäuser, Felix Henningsen, Ryan Hotte, Reyna Jenkyns, Martina Karl, Natasha Khera, Nikhita Khera, Ian Kulin, Alex Lam, Tim Lavallee, Klaus Leismüller, Laszlo Papp, Benoit Pirenne, Emily Price , et al. (14 additional authors not shown)

Abstract: Since 2018, the potential for a high-energy neutrino telescope, named the Pacific Ocean Neutrino Experiment (P-ONE), has been thoroughly examined by two pathfinder missions, STRAW and STRAW-b, short for short for Strings for Absorption Length in Water. The P-ONE project seeks to install a neutrino detector with a one cubic kilometer volume in the Cascadia Basin's deep marine surroundings, situated… ▽ More Since 2018, the potential for a high-energy neutrino telescope, named the Pacific Ocean Neutrino Experiment (P-ONE), has been thoroughly examined by two pathfinder missions, STRAW and STRAW-b, short for short for Strings for Absorption Length in Water. The P-ONE project seeks to install a neutrino detector with a one cubic kilometer volume in the Cascadia Basin's deep marine surroundings, situated near the western shores of Vancouver Island, Canada. To assess the environmental conditions and feasibility of constructing a neutrino detector of that scale, the pathfinder missions, STRAW and STRAW-b, have been deployed at a depth of 2.7 km within the designated site for P-ONE and were connected to the NEPTUNE observatory, operated by Ocean Networks Canada (ONC). While STRAW focused on analyzing the optical properties of water in the Cascadia Basin, \ac{strawb} employed cameras and spectrometers to investigate the characteristics of bioluminescence in the deep-sea environment. This report introduces the STRAW-b concept, covering its scientific objectives and the instrumentation used. Furthermore, it discusses the design considerations implemented to guarantee a secure and dependable deployment process of STRAW-b. Additionally, it showcases the data collected by battery-powered loggers, which monitored the mechanical stress on the equipment throughout the deployment. The report also offers an overview of STRAW-b's operation, with a specific emphasis on the notable advancements achieved in the data acquisition (DAQ) system and its successful integration with the server infrastructure of ONC. △ Less

Submitted 6 February, 2024; v1 submitted 25 October, 2023; originally announced October 2023.

Comments: 20 pages, 11 figures, 2 tables

Defect-induced helicity-dependent terahertz emission in Dirac semimetal PtTe2 thin films

Authors: Zhongqiang Chen, Hongsong Qiu, Xinjuan Cheng, Jizhe Cui, Zuanming Jin, Da Tian, Xu Zhang, Kankan Xu, Ruxin Liu, Wei Niu, Liqi Zhou, Tianyu Qiu, Yequan Chen, Caihong Zhang, Xiaoxiang Xi, Fengqi Song, Rong Yu, Xuechao Zhai, Biaobing Jin, Rong Zhang, Xuefeng Wang

Abstract: Nonlinear transport enabled by symmetry breaking in quantum materials has aroused considerable interest in condensed matter physics and interdisciplinary electronics. However, the nonlinear optical response in centrosymmetric Dirac semimetals via the defect engineering has remained highly challenging. Here, we observe the helicity-dependent terahertz (THz) emission in Dirac semimetal PtTe2 thin fi… ▽ More Nonlinear transport enabled by symmetry breaking in quantum materials has aroused considerable interest in condensed matter physics and interdisciplinary electronics. However, the nonlinear optical response in centrosymmetric Dirac semimetals via the defect engineering has remained highly challenging. Here, we observe the helicity-dependent terahertz (THz) emission in Dirac semimetal PtTe2 thin films via circular photogalvanic effect (CPGE) under normal incidence. This is activated by artificially controllable out-of-plane Te-vacancy defect gradient, which is unambiguously evidenced by the electron ptychography. The defect gradient lowers the symmetry, which not only induces the band spin splitting, but also generates the giant Berry curvature dipole (BCD) responsible for the CPGE. Such BCD-induced helicity-dependent THz emission can be manipulated by the Te-vacancy defect concentration. Furthermore, temperature evolution of the THz emission features the minimum of the THz amplitude due to the carrier compensation. Our work provides a universal strategy for symmetry breaking in centrosymmetric Dirac materials for efficient nonlinear transport and facilitates the promising device applications in integrated optoelectronics and spintronics. △ Less

Submitted 1 March, 2024; v1 submitted 15 October, 2023; originally announced October 2023.

Comments: 27 pages, 5 figures

Journal ref: Nature Communications (2024)

Surface Hopping, Electron Translation Factors, Electron Rotation Factors, Momentum Conservation, and Size Consistency

Authors: Vishikh Athavale, Xuezhi Bian, Zhen Tao, Yanze Wu, Tian Qiu, Jonathan Rawlinson, Robert G. Littlejohn, Joseph E. Subotnik

Abstract: For a system without spin-orbit coupling, the (i) nuclear plus electronic linear momentum and (ii) nuclear plus orbital electronic angular momentum are good quantum numbers. Thus, when a molecular system undergoes a nonadiabatic transition, there should be no change in the total linear or angular momentum. Now, the standard surface hopping algorithm ignores the electronic momentum and indirectly e… ▽ More For a system without spin-orbit coupling, the (i) nuclear plus electronic linear momentum and (ii) nuclear plus orbital electronic angular momentum are good quantum numbers. Thus, when a molecular system undergoes a nonadiabatic transition, there should be no change in the total linear or angular momentum. Now, the standard surface hopping algorithm ignores the electronic momentum and indirectly equates the momentum of the nuclear degrees of freedom to the total momentum. However, even with this simplification, the algorithm still does not conserve either the nuclear linear or the nuclear angular momenta. Here, we show that one way to address these failures is to dress the derivative couplings (i.e. the hopping directions) in two ways: (i) we disallow changes in the nuclear linear momentum by working in a translating basis (which is well known and leads to electron translation factors [ETFs]); and (ii) we disallow changes in the nuclear angular momentum by working in a basis that rotates around the center of mass (which is not well-known and leads to a novel, rotationally removable component of the derivative coupling that we will call electron rotation factors [ERFs] below, cf. Eq. 96). The present findings should be helpful in the short term as far as interpreting surface hopping calculations for singlet systems (without spin) and then developing new surface hopping algorithm in the long term for systems where one cannot ignore the electronic orbital and/or spin angular momentum. △ Less

Submitted 28 August, 2023; originally announced August 2023.

Spectral-temporal-spatial customization via modulating multimodal nonlinear pulse propagation

Authors: Tong Qiu, Honghao Cao, Kunzan Liu, Li-Yu Yu, Manuel Levy, Eva Lendaro, Fan Wang, Sixian You

Abstract: Multimode fibers (MMFs) have recently reemerged as attractive avenues for nonlinear effects due to their high-dimensional spatiotemporal nonlinear dynamics and scalability for high power. High-brightness MMF sources with effective control of the nonlinear processes would offer new possibilities for a wide range of applications from high-power fiber lasers, to bioimaging and chemical sensing, and t… ▽ More Multimode fibers (MMFs) have recently reemerged as attractive avenues for nonlinear effects due to their high-dimensional spatiotemporal nonlinear dynamics and scalability for high power. High-brightness MMF sources with effective control of the nonlinear processes would offer new possibilities for a wide range of applications from high-power fiber lasers, to bioimaging and chemical sensing, and to novel physics phenomena. Here we present a simple yet effective way of controlling nonlinear effects at high peak power levels: by leveraging not only the spatial but also the temporal degrees of freedom of the multimodal nonlinear pulse propagation in step-index MMFs using a programmable fiber shaper. This method represents the first method that enables modulation and optimization of multimodal nonlinear pulse propagation, achieving high tunability and broadband high peak power. Its potential as a nonlinear imaging source is further demonstrated by applying the MMF source to multiphoton microscopy, where widely tunable two-photon and three-photon imaging is achieved with adaptive optimization. These demonstrations highlight the effectiveness of directly modulating multimodal nonlinear pulse propagation to enhance the high-dimensional customization and optimize the high spectral brightness of MMF output. These advancements provide new possibilities for technology advances in nonlinear optics, bioimaging, spectroscopy, optical computing, and material processing. △ Less

Submitted 5 December, 2023; v1 submitted 8 June, 2023; originally announced June 2023.

Comments: 36 pages, 19 figures

STCF Conceptual Design Report: Volume 1 -- Physics & Detector

Authors: M. Achasov, X. C. Ai, R. Aliberti, L. P. An, Q. An, X. Z. Bai, Y. Bai, O. Bakina, A. Barnyakov, V. Blinov, V. Bobrovnikov, D. Bodrov, A. Bogomyagkov, A. Bondar, I. Boyko, Z. H. Bu, F. M. Cai, H. Cai, J. J. Cao, Q. H. Cao, Z. Cao, Q. Chang, K. T. Chao, D. Y. Chen, H. Chen , et al. (413 additional authors not shown)

Abstract: The Super $τ$-Charm facility (STCF) is an electron-positron collider proposed by the Chinese particle physics community. It is designed to operate in a center-of-mass energy range from 2 to 7 GeV with a peak luminosity of $0.5\times 10^{35}{\rm cm}^{-2}{\rm s}^{-1}$ or higher. The STCF will produce a data sample about a factor of 100 larger than that by the present $τ$-Charm factory -- the BEPCII,… ▽ More The Super $τ$-Charm facility (STCF) is an electron-positron collider proposed by the Chinese particle physics community. It is designed to operate in a center-of-mass energy range from 2 to 7 GeV with a peak luminosity of $0.5\times 10^{35}{\rm cm}^{-2}{\rm s}^{-1}$ or higher. The STCF will produce a data sample about a factor of 100 larger than that by the present $τ$-Charm factory -- the BEPCII, providing a unique platform for exploring the asymmetry of matter-antimatter (charge-parity violation), in-depth studies of the internal structure of hadrons and the nature of non-perturbative strong interactions, as well as searching for exotic hadrons and physics beyond the Standard Model. The STCF project in China is under development with an extensive R\&D program. This document presents the physics opportunities at the STCF, describes conceptual designs of the STCF detector system, and discusses future plans for detector R\&D and physics case studies. △ Less

Submitted 5 October, 2023; v1 submitted 28 March, 2023; originally announced March 2023.

Journal ref: Front. Phys. 19(1), 14701 (2024)

Roadmap on Deep Learning for Microscopy

Authors: Giovanni Volpe, Carolina Wählby, Lei Tian, Michael Hecht, Artur Yakimovich, Kristina Monakhova, Laura Waller, Ivo F. Sbalzarini, Christopher A. Metzler, Mingyang Xie, Kevin Zhang, Isaac C. D. Lenton, Halina Rubinsztein-Dunlop, Daniel Brunner, Bijie Bai, Aydogan Ozcan, Daniel Midtvedt, Hao Wang, Nataša Sladoje, Joakim Lindblad, Jason T. Smith, Marien Ochoa, Margarida Barroso, Xavier Intes, Tong Qiu , et al. (50 additional authors not shown)

Abstract: Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the… ▽ More Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences. △ Less

Submitted 7 March, 2023; originally announced March 2023.

Range-Separated Hybrid Functional Pseudopotentials

Authors: Yang Yang, Georgia Prokopiou, Tian Qiu, Aaron M. Schankler, Andrew M. Rappe, Leeor Kronik, Robert A. DiStasio Jr

Abstract: Consistency between the exchange-correlation (xc) functional used during pseudopotential construction and planewave-based electronic structure calculations is important for an accurate and reliable description of the structure and properties of condensed-phase systems. In this work, we present a general scheme for constructing pseudopotentials with range-separated hybrid (RSH) xc functionals based… ▽ More Consistency between the exchange-correlation (xc) functional used during pseudopotential construction and planewave-based electronic structure calculations is important for an accurate and reliable description of the structure and properties of condensed-phase systems. In this work, we present a general scheme for constructing pseudopotentials with range-separated hybrid (RSH) xc functionals based on the solution of the all-electron radial integro-differential equation for a spherical atomic configuration. As proof-of-principle, we demonstrate pseudopotential construction with the PBE, PBE0, HSE, and sRSH (based on LC-$ω$PBE0) xc functionals for a select set of atoms, and then investigate the importance of pseudopotential consistency when computing band gaps, equilibrium lattice parameters, bulk moduli, and atomization energies of several solid-state systems. In doing so, we find that pseudopotential consistency errors (PSCE) tend to be systematic and can be as large as $1.4\%$ when computing these properties. △ Less

Submitted 22 February, 2023; originally announced February 2023.

A CsI hodoscope on CSHINE for Bremsstrahlung γ-rays in Heavy Ion Reactions

Authors: Yuhao Qin, Dong Guo, Sheng Xiao, Yijie Wang, Fenhai Guan, Xinyue Diao, Zhi Qin, Dawei Si, Boyuan Zhang, Yaopeng Zhang, Xianglun Wei, Herun Yang, Peng Ma, Haichuan Zou, Tianli Qiu, Xinjie Huang, Rongjiang Hu, Limin Duan, Fangfang Duan, Qiang Hu, Junbing Ma, Shiwei Xu, Zhen Bai, Yanyun Yang, Zhigang Xiao

Abstract: Bremsstrahlung $γ$ production in heavy ion reactions at Fermi energies carries important physical information including the nuclear symmetry energy at supra-saturation densities. In order to detect the high energy Bremsstrahlung $γ$ rays, a hodoscope consisting of 15 CsI(Tl) crystal read out by photo multiplier tubes has been built, tested and operated in experiment. The resolution, efficiency and… ▽ More Bremsstrahlung $γ$ production in heavy ion reactions at Fermi energies carries important physical information including the nuclear symmetry energy at supra-saturation densities. In order to detect the high energy Bremsstrahlung $γ$ rays, a hodoscope consisting of 15 CsI(Tl) crystal read out by photo multiplier tubes has been built, tested and operated in experiment. The resolution, efficiency and linear response of the units to $γ$ rays have been studied using radioactive source and $({\rm p},γ)$ reactions. The inherent energy resolution of $1.6\%+2\%/E_γ^{1/2}$ is obtained. Reconstruction method has been established through Geant 4 simulations, reproducing the experimental results where comparison can be made. Using the reconstruction method developed, the whole efficiency of the hodoscope is about $2.6\times 10^{-4}$ against the $4π$ emissions at the target position, exhibiting insignificant dependence on the energy of incident $γ$ rays above 20 MeV. The hodoscope is operated in the experiment of $^{86}$Kr + $^{124}$Sn at 25 MeV/u, and a full $γ$ energy spectrum up to 80 MeV has been obtained. △ Less

Submitted 27 December, 2022; originally announced December 2022.

Comments: 9 pages, 19 figures

Symmetric Post-Transition-State Bifurcation Reactions with Berry Pseudo-Magnetic Fields

Authors: Zhen Tao, Tian Qiu, Joseph E. Subotnik

Abstract: We investigate how the Berry force (i.e. the pseudo-magnetic force operating on nuclei as induced by electronic degeneracy and spin-orbit coupling (SOC)) might modify a post-transition state bifurcation (PTSB) reaction path and affect product selectivity for situations when multiple products share the same transition state. To estimate the magnitude of this effect, Langevin dynamics are performed… ▽ More We investigate how the Berry force (i.e. the pseudo-magnetic force operating on nuclei as induced by electronic degeneracy and spin-orbit coupling (SOC)) might modify a post-transition state bifurcation (PTSB) reaction path and affect product selectivity for situations when multiple products share the same transition state. To estimate the magnitude of this effect, Langevin dynamics are performed on a model system with a valley-ridge inflection (VRI) point in the presence of a magnetic field (that mimics the Berry curvature). We also develop an analytic model for such selectivity that depends on key parameters such as the surface topology, the magnitude of the Berry force, and the nuclear friction. Within this dynamical model, static electronic structure calculations (at the level of generalized Hartree-Fock with spin-orbit coupling (GHF+SOC) theory) suggest that electronic-spin induced Berry force effects may indeed lead to noticeable changes in methoxy radical isomerization. △ Less

Submitted 14 November, 2022; originally announced November 2022.

Completely Spin-Decoupled Geometric Phase of Metasurface

Authors: Xinmin Fu, Jie Yang, Jiafu Wang, Yajuan Han, Chang Ding, Tianshuo Qiu, Bingyue Qu, Lei Li, Yongfeng Li, Shaobo Qu

Abstract: Metasurfaces have provided unprecedented degree of freedom (DOF) in manipulating electromagnetic (EM) waves. Geometric phase can be readily obtained by rotating the meta-atom of metasurfaces. Nevertheless, such geometric phases are usually spin-coupled, with the same magnitude but opposite signs for left_ and right_handed circularly polarized (LCP,RCP) waves. To achieve independent control on LCP… ▽ More Metasurfaces have provided unprecedented degree of freedom (DOF) in manipulating electromagnetic (EM) waves. Geometric phase can be readily obtained by rotating the meta-atom of metasurfaces. Nevertheless, such geometric phases are usually spin-coupled, with the same magnitude but opposite signs for left_ and right_handed circularly polarized (LCP,RCP) waves. To achieve independent control on LCP and RCP waves, it is crucial to obtain spin-decoupled geometric phases. In this paper, we propose to obtain completely spin-decoupled geometric phases by engineering surface current paths on meta-atoms. Based on the rotational Doppler effect, the rotation manner is firstly analyzed and it is found that the essence of generating geometric phase lies in the rotation of surface current paths on meta-atoms. Since the induced surface currents paths under LCP and RCP waves always start oppositely and are mirror-symmetrical with each other, it is natural that the geometric phases be with the same magnitude and opposite signs when the meta-atoms are rotated. To obtain spin-decoupled geometric phases, the start point of induced surface current under one spin should be rotated by an angle while that under the other spin by another different angle. In this way, LCP and RCP waves can acquire different geometric phase changes and spin-decoupled geometric phase can be imparted by metasurfaces. Proof-of-principle prototypes were designed, fabricated and measured. Both the simulation and experiment results verify spin-decoupled geometric phases. This work provides a robust means of obtaining spin-dependent geometric phase and will further adds up to the metasurface DOF in manipulating EM waves. △ Less

Submitted 1 August, 2022; originally announced August 2022.

An FPGA-based Trigger System for CSHINE

Authors: Dong Guo, Yuhao Qin, Sheng Xiao, Zhi Qin, Yijie Wang, Fenhai Guan, Xinyue Diao, Boyuan Zhang, Yaopeng Zhang, Dawei Si, Shiwei Xu, Xianglun Wei, Herun Yang, Peng Ma, Tianli Qiu, Haichuan Zou, Limin Duan, Zhigang Xiao

Abstract: A trigger system of general function is designed using the commercial module CAEN V2495 for heavy ion nuclear reaction experiment at Fermi energies. The system has been applied and verified on CSHINE (Compact Spectrometer for Heavy IoN Experiment). Based on the field programmable logic gate array (FPGA) technology of command register access and remote computer control operation, trigger functions… ▽ More A trigger system of general function is designed using the commercial module CAEN V2495 for heavy ion nuclear reaction experiment at Fermi energies. The system has been applied and verified on CSHINE (Compact Spectrometer for Heavy IoN Experiment). Based on the field programmable logic gate array (FPGA) technology of command register access and remote computer control operation, trigger functions can be flexibly configured according to the experimental physical goals. Using the trigger system on CSHINE, we carried out the beam experiment of 25 MeV/u $ ^{86}{\rm Kr}+ ^{124}{\rm Sn}$ on the Radioactive Ion Beam Line 1 in Lanzhou (RIBLL1), China. The online results demonstrate that the trigger system works normally and correctly. The system can be extended to other experiments. △ Less

Submitted 30 June, 2022; originally announced June 2022.

Structural engineering of transition-metal nitrides for surface-enhanced Raman scattering chips

Authors: Leilei Lan, Haorun Yao, Guoqun Li, Xingce Fan, Mingze Li, Teng Qiu

Abstract: Noble-metal-free surface-enhanced Raman scattering (SERS) substrates have attracted great attention for their abundant sources, good signal uniformity, superior biocompatibility, and high chemical stability. However, the lack of controllable synthesis and fabrication of noble-metal-free substrates with high SERS activity impedes their practical applications. Herein,we propose a general strategy to… ▽ More Noble-metal-free surface-enhanced Raman scattering (SERS) substrates have attracted great attention for their abundant sources, good signal uniformity, superior biocompatibility, and high chemical stability. However, the lack of controllable synthesis and fabrication of noble-metal-free substrates with high SERS activity impedes their practical applications. Herein,we propose a general strategy to fabricate a series of planar transition-metal nitride (TMN) SERS chips via an ambient temperature sputtering deposition route.These planar TMN (tungsten nitride, tantalum nitride, and molybdenum nitride) chips show remarkable Raman enhancement factors (EFs) with ~105 owing to efficient photoinduced charge transfer process between TMN chips and probe molecules. Further, structural engineering of these TMN chips is used to improve their SERS activity. Benefiting from the synergistic effect of charge transfer process and electric field enhancement by constructing nanocavity structure, the Raman EF of WN nanocavity chips could be greatly improved to 1.29 * 107, which is an order of magnitude higher than that of planar chips. Moreover, we also design the WN/monolayer MoS2 heterostructure chips. With the increase of surface electron density on the upper WN and more exciton resonance transitions in the heterostructure, a 1.94 * 107 level EF and a 5 * 10-10 m level detention limit could be achieved. Our results provide important guidance for the structural design of ultrasensitive noble-metal-free SERS chips. △ Less

Submitted 12 April, 2022; v1 submitted 9 April, 2022; originally announced April 2022.

Journal ref: Nano Research, 15(4), 3794-3803 (2022)

On the Meaning of Berry Force For Unrestricted Systems Treated With Mean-Field Electronic Structure

Authors: Xuezhi Bian, Tian Qiu, Junhan Chen, Joseph E. Subotnik

Abstract: We show that the Berry force as computed by an approximate, mean-field electronic structure can be meaningful if properly interpreted. In particular, for a model Hamiltonian representing a molecular system with an even number of electrons interacting via a two-body (Hubbard) interaction and a spin-orbit coupling, we show that a meaningful nonzero Berry force emerges whenever there is spin unrestri… ▽ More We show that the Berry force as computed by an approximate, mean-field electronic structure can be meaningful if properly interpreted. In particular, for a model Hamiltonian representing a molecular system with an even number of electrons interacting via a two-body (Hubbard) interaction and a spin-orbit coupling, we show that a meaningful nonzero Berry force emerges whenever there is spin unrestriction--even though the Hamiltonian is real-valued and formally the on-diagonal single-surface Berry force must be zero. Moreover, if properly applied, this mean-field Berry force yields roughly the correct asymptotic motion for scattering through an avoided crossing. That being said, within the context of a ground-state calculation, several nuances do arise as far interpreting the Berry force correctly, and as a practical matter, the Berry force diverges near the Coulson-Fisher point (which can lead to numerical instabilities). We do not address magnetic fields here. △ Less

Submitted 28 March, 2022; v1 submitted 25 March, 2022; originally announced March 2022.

Journal ref: J. Chem. Phys. 156, 234107 (2022)

High-Performance Permanent Magnet Array Design by a Fast Genetic Algorithm (GA)-based Optimization for Low-Field Portable MRI

Authors: Ting-Ou Liang, Yan Hao Koh, Tie Qiu, Erping Li, Wenwei Yu, Shao Ying Huang

Abstract: A permanent magnet array (PMA) is a preferred source of magnetic field for body-part-dedicated low-field (<0.5 T) portable magnetic resonance imaging (MRI) because it has a small footprint, no power consumption, and no need for a cooling system. The current popular PMA is limited by the transversal field below 100 mT, where advanced technologies developed for the long-bore MRI systems (e.g., multi… ▽ More A permanent magnet array (PMA) is a preferred source of magnetic field for body-part-dedicated low-field (<0.5 T) portable magnetic resonance imaging (MRI) because it has a small footprint, no power consumption, and no need for a cooling system. The current popular PMA is limited by the transversal field below 100 mT, where advanced technologies developed for the long-bore MRI systems (e.g., multi-channel techniques) cannot be applied. In this paper, a sparse high-performance PMA is proposed based on inward-outward ring pairs and using magnet blocks that can be bought off the shelf, targeting on portable head imaging. Through a fast genetic algorithm (GA)-based optimization, the proposed PMA has a longitudinal magnetic field with an average field strength of 111.40 mT and a monotonic field pattern with inhomogeneity of 10.57 mT (an RF bandwidth of <10%) within a Field of View (FoV) of 20 cm in diameter and 4.5 cm in length. The resulting field was validated using analytic calculations and numerical simulations. The encoding capability of the designed PMA was examined by checking the quality of the simulated reconstructed images. The proposed field outperforms a linear pattern for encoding. The PMA is 57.91 cm wide, 38 cm long, has a 5-gauss range of 87x87x104 cm^3, allowing an operation in a small space. It weights 126.08kg, comprising of a stationary main array that supplies a strong homogeneous field, and a light rotatable sub-gradient-array (5.12kg) that supplies a monotonic field for signal encoding. It has a magnetic field generation efficiency of 0.88mT/kg, the highest among sparse PMAs that offer a monotonic field pattern. The force experienced by each magnet was calculated to validate the feasibility of physical implementation. The proposed PMA can be a promising alternative to supply the main and gradient fields combined for dedicated portable MRI. △ Less

Submitted 23 September, 2021; originally announced September 2021.

XCloud-VIP: Virtual Peak Enables Highly Accelerated NMR Spectroscopy and Faithful Quantitative Measures

Authors: Di Guo, Zhangren Tu, Yi Guo, Yirong Zhou, Jian Wang, Zi Wang, Tianyu Qiu, Min Xiao, Yinran Chen, Liubin Feng, Yuqing Huang, Donghai Lin, Qing Hong, Amir Goldbourt, Meijin Lin, Xiaobo Qu

Abstract: Nuclear Magnetic Resonance (NMR) spectroscopy is an important bio-engineering tool to determine the metabolic concentrations, molecule structures and so on. The data acquisition time, however, is very long in multi-dimensional NMR. To accelerate data acquisition, non-uniformly sampling is an effective way but may encounter severe spectral distortions and unfaithful quantitative measures when the a… ▽ More Nuclear Magnetic Resonance (NMR) spectroscopy is an important bio-engineering tool to determine the metabolic concentrations, molecule structures and so on. The data acquisition time, however, is very long in multi-dimensional NMR. To accelerate data acquisition, non-uniformly sampling is an effective way but may encounter severe spectral distortions and unfaithful quantitative measures when the acceleration factor is high. By modelling the acquired signal as the superimposed exponentials, we proposed a virtual peak (VIP) approach to selfadapt the prior spectral information, such as the resonance frequency and peak lineshape, and then feed these information into the reconstruction. The proposed method is further implemented with cloud computing to facilitate online, open, and easy access. Results on simulated and experimental data demonstrate that, compared with the low-rank Hankel matrix method, the new approach reconstructs high-fidelity NMR spectra from highly undersampled data and achieves more accurate quantification. The maximum quantitative errors of distances between nuclear pairs and concentrations of metabolites in mixtures have been reduced by 61.1% and 57.7%, respectively. △ Less

Submitted 19 October, 2023; v1 submitted 22 March, 2021; originally announced March 2021.

A Spontaneously Formed Plasmonic-MoTe2 Hybrid Platform for Ultrasensitive Raman Enhancement

Authors: Li Tao, Zhiyong Li, Kun Chen, Yaoqiang Zhou, Hao Li, Ximiao Wang, Runze Zhan, Xiangyu Hou, Yu Zhao, Junling Xu, Teng Qiu, Xi Wan, Jian-Bin Xu

Abstract: To develop highly sensitive, stable and repeatable surface-enhanced Raman scattering (SERS) substrates is crucial for analytical detection, which is a challenge for traditional metallic structures. Herein, by taking advantage of the high surface activity of 1T' transition metal telluride, we have fabricated high-density gold nanoparticles (AuNPs) that are spontaneously in-situ prepared on the 1T'… ▽ More To develop highly sensitive, stable and repeatable surface-enhanced Raman scattering (SERS) substrates is crucial for analytical detection, which is a challenge for traditional metallic structures. Herein, by taking advantage of the high surface activity of 1T' transition metal telluride, we have fabricated high-density gold nanoparticles (AuNPs) that are spontaneously in-situ prepared on the 1T' MoTe2 atomic layers via a facile method, forming a plasmonic-2D material hybrid SERS substrate. This AuNP formation is unique to the 1T' phase, which is repressed in 2H MoTe2 with less surface activity. The hybrid structure generates coupling effects of electromagnetic and chemical enhancements, as well as excellent molecule adsorption, leading to the ultrasensitive (4*10^-17 M) and reproducible detection. Additionally, the immense fluorescence and photobleaching phenomena are mostly avoided. Flexible SERS tapes have been demonstrated in practical applications. Our approach facilitates the ultrasensitive SERS detection by a facile method, as well as the better mechanistic understanding of SERS beyond plasmonic effects. △ Less

Submitted 28 July, 2021; v1 submitted 28 February, 2021; originally announced March 2021.

Journal ref: Cell Reports Physical Science, 2021, 2, 100526

Magnetic Resonance Spectroscopy Deep Learning Denoising Using Few In Vivo Data

Authors: Dicheng Chen, Wanqi Hu, Huiting Liu, Yirong Zhou, Tianyu Qiu, Yihui Huang, Zi Wang, Jiazheng Wang, Liangjie Lin, Zhigang Wu, Hao Chen, Xi Chen, Gen Yan, Di Guo, Jianzhong Lin, Xiaobo Qu

Abstract: Magnetic Resonance Spectroscopy (MRS) is a noninvasive tool to reveal metabolic information. One challenge of 1H-MRS is the low Signal-Noise Ratio (SNR). To improve the SNR, a typical approach is to perform Signal Averaging (SA) with M repeated samples. The data acquisition time, however, is increased by M times accordingly, and a complete clinical MRS scan takes approximately 10 minutes at a comm… ▽ More Magnetic Resonance Spectroscopy (MRS) is a noninvasive tool to reveal metabolic information. One challenge of 1H-MRS is the low Signal-Noise Ratio (SNR). To improve the SNR, a typical approach is to perform Signal Averaging (SA) with M repeated samples. The data acquisition time, however, is increased by M times accordingly, and a complete clinical MRS scan takes approximately 10 minutes at a common setting M=128. Recently, deep learning has been introduced to improve the SNR but most of them use the simulated data as the training set. This may hinder the MRS applications since some potential differences, such as acquisition system imperfections, and physiological and psychologic conditions may exist between the simulated and in vivo data. Here, we proposed a new scheme that purely used the repeated samples of realistic data. A deep learning model, Refusion Long Short-Term Memory (ReLSTM), was designed to learn the mapping from the low SNR time-domain data (24 SA) to the high SNR one (128 SA). Experiments on the in vivo brain spectra of 7 healthy subjects, 2 brain tumor patients and 1 cerebral infarction patient showed that only using 20% repeated samples, the denoised spectra by ReLSTM could provide comparable estimated concentrations of metabolites to 128 SA. Compared with the state-of-the-art low-rank denoising method, the ReLSTM achieved the lower relative error and the Cramér-Rao lower bounds in quantifying some important biomarkers. In summary, ReLSTM can perform high-fidelity denoising of the spectra under fast acquisition (24 SA), which would be valuable to MRS clinical studies. △ Less

Submitted 25 October, 2022; v1 submitted 26 January, 2021; originally announced January 2021.

The origin of ultrasensitive SERS sensing beyond plasmonics

Authors: Leilei Lan, Yimeng Gao, Xingce Fan, Mingze Li, Qi Hao, Teng Qiu

Abstract: Plasmon-free surface-enhanced Raman scattering (SERS) substrates have attracted tremendous attention for their abundant sources, excellent chemical stability, superior biocompatibility, good signal uniformity, and unique selectivity to target molecules. Recently, researchers have made great progress in fabricating novel plasmon-free SERS substrates and exploring new enhancement strategies to impro… ▽ More Plasmon-free surface-enhanced Raman scattering (SERS) substrates have attracted tremendous attention for their abundant sources, excellent chemical stability, superior biocompatibility, good signal uniformity, and unique selectivity to target molecules. Recently, researchers have made great progress in fabricating novel plasmon-free SERS substrates and exploring new enhancement strategies to improve their sensitivity. This review summarizes the recent developments of plasmon-free SERS substrates and specially focuses on the enhancement mechanisms and strategies. Furthermore, the promising applications of plasmon-free SERS substrates in biomedical diagnosis, metal ions and organic pollutants sensing, chemical and biochemical reactions monitoring, and photoelectric characterization are introduced. Finally, current challenges and future research opportunities in plasmon-free SERS substrates are briefly discussed. △ Less

Submitted 9 June, 2021; v1 submitted 17 January, 2021; originally announced January 2021.

Journal ref: Front. Phys. 16(4), 43300 (2021)

Hardware Acceleration of HPC Computational Flow Dynamics using HBM-enabled FPGAs

Authors: Tom Hogervorst, Tong Dong Qiu, Giacomo Marchiori, Alf Birger, Markus Blatt, Razvan Nane

Abstract: Scientific computing is at the core of many High-Performance Computing applications, including computational flow dynamics. Because of the uttermost importance to simulate increasingly larger computational models, hardware acceleration is receiving increased attention due to its potential to maximize the performance of scientific computing. A Field-Programmable Gate Array is a reconfigurable hardw… ▽ More Scientific computing is at the core of many High-Performance Computing applications, including computational flow dynamics. Because of the uttermost importance to simulate increasingly larger computational models, hardware acceleration is receiving increased attention due to its potential to maximize the performance of scientific computing. A Field-Programmable Gate Array is a reconfigurable hardware accelerator that is fully customizable in terms of computational resources and memory storage requirements of an application during its lifetime. Therefore, it is an ideal candidate to accelerate scientific computing applications because of the possibility to fully customize the memory hierarchy important in irregular applications such as iterative linear solvers found in scientific libraries. In this paper, we study the potential of using FPGA in HPC because of the rapid advances in reconfigurable hardware, such as the increase in on-chip memory size, increasing number of logic cells, and the integration of High-Bandwidth Memories on board. To perform this study, we first propose a novel ILU0 preconditioner tightly integrated with a BiCGStab solver kernel designed using a mixture of High-Level Synthesis and Register-Transfer Level hand-coded design. Second, we integrate the developed preconditioned iterative solver in Flow from the Open Porous Media (OPM) project, a state-of-the-art open-source reservoir simulator. Finally, we perform a thorough evaluation of the FPGA solver kernel in both standalone mode and integrated into the reservoir simulator that includes all the on-chip URAM and BRAM, on-board High-Bandwidth Memory, and off-chip CPU memory data transfers required in a complex simulator software such as OPM's Flow. We evaluate the performance on the Norne field, a real-world case reservoir model using a grid with more than 10^5 cells and using 3 unknowns per cell. △ Less

Submitted 5 January, 2021; originally announced January 2021.

Report number: Article No.: 20, pp 1--35

Journal ref: ACM Transactions on Reconfigurable Technology and Systems, Volume 15, Issue 2, June 2022

Evolutionary dynamics in financial markets with heterogeneities in strategies and risk tolerance

Authors: Wen-Juan Xu, Chen-Yang Zhong, Fei Ren, Tian Qiu, Rong-Da Chen, Yun-Xin He, Li-Xin Zhong

Abstract: In nature and human societies, the effects of homogeneous and heterogeneous characteristics on the evolution of collective behaviors are quite different from each other. It is of great importance to understand the underlying mechanisms of the occurrence of such differences. By incorporating pair pattern strategies and reference point strategies into an agent-based model, we have investigated the c… ▽ More In nature and human societies, the effects of homogeneous and heterogeneous characteristics on the evolution of collective behaviors are quite different from each other. It is of great importance to understand the underlying mechanisms of the occurrence of such differences. By incorporating pair pattern strategies and reference point strategies into an agent-based model, we have investigated the coupled effects of heterogeneous investment strategies and heterogeneous risk tolerance on price fluctuations. In the market flooded with the investors with homogeneous investment strategies or homogeneous risk tolerance, large price fluctuations are easy to occur. In the market flooded with the investors with heterogeneous investment strategies or heterogeneous risk tolerance, the price fluctuations are suppressed. For a heterogeneous population, the coexistence of investors with pair pattern strategies and reference point strategies causes the price to have a slow fluctuation around a typical equilibrium point and both a large price fluctuation and a no-trading state are avoided, in which the pair pattern strategies push the system far away from the equilibrium while the reference point strategies pull the system back to the equilibrium. A theoretical analysis indicates that the evolutionary dynamics in the present model is governed by the competition between different strategies. The strategy that causes large price fluctuations loses more while the strategy that pulls the system back to the equilibrium gains more. Overfrequent trading does harm to one's pursuit for more wealth. △ Less

Submitted 18 October, 2020; originally announced October 2020.

Coupled effects of epidemic information and risk awareness on contagion

Authors: Wen-Juan Xu, Chen-Yang Zhong, Hui-Fen Ye, Rong-Da Chen, Tian Qiu, Fei Ren, Li-Xin Zhong

Abstract: By incorporating delayed epidemic information and self-restricted travel behavior into the SIS model, we have investigated the coupled effects of timely and accurate epidemic information and people's sensitivity to the epidemic information on contagion. In the population with only local random movement, whether the epidemic information is delayed or not has no effect on the spread of the epidemic.… ▽ More By incorporating delayed epidemic information and self-restricted travel behavior into the SIS model, we have investigated the coupled effects of timely and accurate epidemic information and people's sensitivity to the epidemic information on contagion. In the population with only local random movement, whether the epidemic information is delayed or not has no effect on the spread of the epidemic. People's high sensitivity to the epidemic information leads to their risk aversion behavior and the spread of the epidemic is suppressed. In the population with only global person-to-person movement, timely and accurate epidemic information helps an individual cut off the connections with the infected in time and the epidemic is brought under control in no time. A delay in the epidemic information leads to an individual's misjudgment of who has been infected and who has not, which in turn leads to rapid progress and a higher peak of the epidemic. In the population with coexistence of local and global movement, timely and accurate epidemic information and people's high sensitivity to the epidemic information play an important role in curbing the epidemic. A theoretical analysis indicates that people's misjudgment caused by the delayed epidemic information leads to a higher encounter probability between the susceptible and the infected and people's self-restricted travel behavior helps reduce such an encounter probability. A functional relation between the ratio of infected individuals and the susceptible-infected encounter probability has been found. △ Less

Submitted 14 September, 2020; v1 submitted 11 September, 2020; originally announced September 2020.

Review and Prospect: NMR Spectroscopy Denoising & Reconstruction with Low Rank Hankel Matrices and Tensors

Authors: Tianyu Qiu, Zi Wang, Huiting Liu, Di Guo, Xiaobo Qu

Abstract: Nuclear Magnetic Resonance (NMR) spectroscopy is an important analytical tool in chemistry, biology, and life science, but it suffers from relatively low sensitivity and long acquisition time. Thus, improving the apparent signal-to-noise ratio and accelerating data acquisition become indispensable. In this review, we summarize the recent progress on low rank Hankel matrix and tensor methods, that… ▽ More Nuclear Magnetic Resonance (NMR) spectroscopy is an important analytical tool in chemistry, biology, and life science, but it suffers from relatively low sensitivity and long acquisition time. Thus, improving the apparent signal-to-noise ratio and accelerating data acquisition become indispensable. In this review, we summarize the recent progress on low rank Hankel matrix and tensor methods, that exploit the exponential property of free induction decay signals, to enable effective denoising and spectra reconstruction. We also outline future developments that are likely to make NMR spectroscopy a far more powerful technique. △ Less

Submitted 16 July, 2020; originally announced July 2020.

Comments: 13 pages, 21 figures, 9 tables

An auto-parameter denoising method for nuclear magnetic resonance spectroscopy based on low-rank Hankel matrix

Authors: Tianyu Qiu, Wenjing Liao, Di Guo, Dongbao Liu, Xin Wang, Jian-Feng Cai, Xiaobo Qu

Abstract: Nuclear Magnetic Resonance (NMR) spectroscopy, which is modeled as the sum of damped exponential signals, has become an indispensable tool in various scenarios, such as the structure and function determination, chemical analysis, and disease diagnosis. NMR spectroscopy signals, however, are usually corrupted by Gaussian noise in practice, raising difficulties in sequential analysis and quantificat… ▽ More Nuclear Magnetic Resonance (NMR) spectroscopy, which is modeled as the sum of damped exponential signals, has become an indispensable tool in various scenarios, such as the structure and function determination, chemical analysis, and disease diagnosis. NMR spectroscopy signals, however, are usually corrupted by Gaussian noise in practice, raising difficulties in sequential analysis and quantification of the signals. The low-rank Hankel property plays an important role in the denoising issue, but selecting an appropriate parameter still remains a problem. In this work, we explore the effect of the regularization parameter of a convex optimization denoising method based on low-rank Hankel matrices for exponential signals corrupted by Gaussian noise. An accurate estimate on the spectral norm of weighted Hankel matrices is provided as a guidance to set the regularization parameter. The bound can be efficiently calculated since it only depends on the standard deviation of the noise and a constant. Aided by the bound, one can easily obtain an auto-setting regularization parameter to produce promising denoised results. Our experiments on synthetic and realistic NMR spectroscopy data demonstrate a superior denoising performance of our proposed approach in comparison with the typical Cadzow and the state-of-the-art QR decomposition methods, especially in the low signal-to-noise ratio regime. △ Less

Submitted 14 November, 2020; v1 submitted 30 January, 2020; originally announced January 2020.

A Robust and Unified Solution for Choosing the Phases of Adiabatic States as a Function of Geometry: Extending Parallel Transport Concepts to the cases of Trivial & Near Trivial Crossings

Authors: Zeyu Zhou, Zuxin Jin, Tian Qiu, Andrew M. Rappe, Joseph Eli Subotnik

Abstract: We investigate a simple and robust scheme for choosing the phases of adiabatic electronic states smoothly (as a function of geometry) so as to maximize the performance of ab initio non-adiabatic dynamics methods. Our approach is based upon consideration of the overlap matrix ($\mathbf{U}$) between basis functions at successive points in time and selecting the phases so as to minimize the matrix no… ▽ More We investigate a simple and robust scheme for choosing the phases of adiabatic electronic states smoothly (as a function of geometry) so as to maximize the performance of ab initio non-adiabatic dynamics methods. Our approach is based upon consideration of the overlap matrix ($\mathbf{U}$) between basis functions at successive points in time and selecting the phases so as to minimize the matrix norm of $\log(\mathbf{U})$. In so doing, one can extend the concept of parallel transport to cases with sharp curve crossings. We demonstrate that this algorithm performs well under extreme situations where dozens of states cross each other either through trivial crossings (where there is zero effective diabatic coupling), or through nontrivial crossings (when there is a nonzero diabatic coupling), or through a combination of both. In all cases, we compute the time-derivative coupling matrix elements (or equivalently non-adiabatic derivative coupling matrix elements) that are as smooth as possible. Our results should be of interest to all who are interested in either non-adiabatic dynamics, or more generally, parallel transport in large systems. △ Less

Submitted 24 September, 2019; originally announced September 2019.

Comments: 29 pages, 2 figures

Multiple learning mechanisms promote cooperation in public goods games with project selection

Authors: Li-Xin Zhong, Wen-Juan Xu, Rong-Da Chen, Yun-Xin He, Tian Qiu, Fei Ren, Yong-Dong Shi, Chen-Yang Zhong

Abstract: How evolution favors cooperation is a fundamental issue in social and economic systems. In the business world, actively selecting a suitable project is usually helpful for a businessman to be in an advantageous position. By incorporating project selection mechanism into the threshold public goods game, we have investigated the coupling effect of mutation and imitation in updating one's preferred p… ▽ More How evolution favors cooperation is a fundamental issue in social and economic systems. In the business world, actively selecting a suitable project is usually helpful for a businessman to be in an advantageous position. By incorporating project selection mechanism into the threshold public goods game, we have investigated the coupling effect of mutation and imitation in updating one's preferred project scale on the evolution of cooperation. Compared with the situation where there is no project selection mechanism, the existence of project selection may suppress or promote cooperation depending upon different updating rules. There exists a critical ratio of the imitators in the population, below which cooperation is suppressed while above which cooperation is promoted. With the coevolving of individual strategies and preferred project scales, a higher level of cooperation corresponds to a larger average value of the preferred project scales. A theoretical analysis indicates that, as most of the individuals are mutants, the coevolving process is governed by the mutation process, which leads to a smaller average value of the preferred project scales and a lower level of cooperation. As most of the individuals are imitators, the coevolving process is governed by the coupling of the mutation and imitation processes, which leads to a larger average value of the preferred project scales and a higher level of cooperation. As all the individuals are imitators, the coevolving process is governed by the imitation process, which leads to an intermediate average value of the preferred project scales and an intermediate level of cooperation. △ Less

Submitted 21 November, 2019; v1 submitted 15 June, 2019; originally announced June 2019.

Accelerated Nuclear Magnetic Resonance Spectroscopy with Deep Learning

Authors: Xiaobo Qu, Yihui Huang, Hengfa Lu, Tianyu Qiu, Di Guo, Tatiana Agback, Vladislav Orekhov, Zhong Chen

Abstract: Nuclear magnetic resonance (NMR) spectroscopy serves as an indispensable tool in chemistry and biology but often suffers from long experimental time. We present a proof-of-concept of application of deep learning and neural network for high-quality, reliable, and very fast NMR spectra reconstruction from limited experimental data. We show that the neural network training can be achieved using solel… ▽ More Nuclear magnetic resonance (NMR) spectroscopy serves as an indispensable tool in chemistry and biology but often suffers from long experimental time. We present a proof-of-concept of application of deep learning and neural network for high-quality, reliable, and very fast NMR spectra reconstruction from limited experimental data. We show that the neural network training can be achieved using solely synthetic NMR signal, which lifts the prohibiting demand for a large volume of realistic training data usually required in the deep learning approach. △ Less

Submitted 14 May, 2019; v1 submitted 9 April, 2019; originally announced April 2019.

Comments: 23 pages, 23 figures, 3 tables

Integrated Waveguide Brillouin Laser

Authors: Sarat Gundavarapu, Matthew Puckett, Taran Huffman, Ryan Behunin, Jianfeng Wu, Tiequn Qiu, Grant M. Brodnik, Cátia Pinho, Debapam Bose, Peter T. Rakich, Jim Nohava, Karl D. Nelson, Mary Salit, Daniel J. Blumenthal

Abstract: The demand for high-performance chip-scale lasers has driven rapid growth in integrated photonics. The creation of such low-noise laser sources is critical for emerging on-chip applications, ranging from coherent optical communications, photonic microwave oscillators remote sensing and optical rotational sensors. While Brillouin lasers are a promising solution to these challenges, new strategies a… ▽ More The demand for high-performance chip-scale lasers has driven rapid growth in integrated photonics. The creation of such low-noise laser sources is critical for emerging on-chip applications, ranging from coherent optical communications, photonic microwave oscillators remote sensing and optical rotational sensors. While Brillouin lasers are a promising solution to these challenges, new strategies are needed to create robust, compact, low power and low cost Brillouin laser technologies through wafer-scale integration. To date, chip-scale Brillouin lasers have remained elusive due to the difficulties in realization of these lasers on a commercial integration platform. In this paper, we demonstrate, for the first time, monolithically integrated Brillouin lasers using a wafer-scale process based on an ultra-low loss Si3N4/SiO2 waveguide platform. Cascading of stimulated Brillouin lasing to 10 Stokes orders was observed in an integrated bus-coupled resonator with a loaded Q factor exceeding 28 million. We experimentally quantify the laser performance, including threshold, slope efficiency and cascading dynamics, and compare the results with theory. The large mode volume integrated resonator and gain medium supports a TE-only resonance and unique 2.72 GHz free spectral range, essential for high performance integrated Brillouin lasing. The laser is based on a non-acoustic guiding design that supplies a broad Brillouin gain bandwidth. Characteristics for high performance lasing are demonstrated due to large intra-cavity optical power and low lasing threshold power. Consistent laser performance is reported for multiple chips across multiple wafers. This design lends itself to wafer-scale integration of practical high-yield, highly coherent Brillouin lasers on a chip. △ Less

Submitted 13 September, 2017; originally announced September 2017.

Comments: 15 pages, 6 figures, methods

Journal ref: nature.photon 13 (2019) 60-67

The role of symmetry in driven propulsion at low Reynolds number

Authors: Johannes Sachs, Konstantin I. Morozov, Oded Kenneth, Tian Qiu, Nico Segreto, Peer Fischer, Alexander M. Leshansky

Abstract: We theoretically and experimentally investigate low-Reynolds-number propulsion of geometrically achiral planar objects that possess a dipole moment and that are driven by a rotating magnetic field. Symmetry considerations (involving parity, $\widehat{P}$, and charge conjugation, $\widehat{C}$) establish correspondence between propulsive states depending on orientation of the dipolar moment. Althou… ▽ More We theoretically and experimentally investigate low-Reynolds-number propulsion of geometrically achiral planar objects that possess a dipole moment and that are driven by a rotating magnetic field. Symmetry considerations (involving parity, $\widehat{P}$, and charge conjugation, $\widehat{C}$) establish correspondence between propulsive states depending on orientation of the dipolar moment. Although basic symmetry arguments do not forbid individual symmetric objects to efficiently propel due to spontaneous symmetry breaking, they suggest that the average ensemble velocity vanishes. Some additional arguments show, however, that highly symmetrical ($\widehat{P}$-even) objects exhibit no net propulsion while individual less symmetrical ($\widehat{C}\widehat{P}$-even) propellers do propel. Particular magnetization orientation, rendering the shape $\widehat{C}\widehat{P}$-odd, yields unidirectional motion typically associated with chiral structures, such as helices. If instead of a structure with a permanent dipole we consider a polarizable object, some of the arguments have to be modified. For instance, we demonstrate a truly achiral ($\widehat{P}$- and $\widehat{C}\widehat{P}$-even) planar shape with an induced electric dipole that can propel by electro-rotation. We thereby show that chirality is not essential for propulsion due to rotation-translation coupling at low Reynolds number. △ Less

Submitted 19 March, 2019; v1 submitted 3 August, 2017; originally announced August 2017.

Comments: 5 pages, 5 figures

Journal ref: Phys. Rev. E 98, 063105 (2018)