arXiv subjects

Jinzhen Zhu

Publications and source records attributed to Jinzhen Zhu.

11 recordsLinked to original sources

arXiv2026

Quantum Dynamics of $H_2^+$ in Orthogonal Two-Color Fields

We present full-dimensional quantum simulations of $H_2^+$ dissociative ionization driven by strong orthogonal laser fields. We consider equal-frequency orthogonal components, which generate elliptical or circular polarization depending on their relative phase and amplitude, as well as orthogonal $800$- and $400$-nm two-color fields. These two-dimensional fields strongly modify the fragmentation dynamics. Most notably, we identify a high-energy peak in the proton kinetic-energy-release (KER) spectrum at approximately $4-5$ eV that is absent from the corresponding single-color, linearly polarized calculations. The yield of this peak can be coherently controlled by varying the relative carrier-envelope phase of the perpendicular field component. The perpendicular field also disrupts the clear electron-proton energy-sharing pattern observed in the main $3-3.5$ eV dissociation channel, indicating more complex multichannel dynamics. Time-dependent state projections and calculations initiated from individual excited states attribute the additional peak to laser-induced vibrational excitation of $H_2^+$. Furthermore, the perpendicular field rotates the fragment angular distributions, causing the most probable proton and electron emission directions to deviate substantially from the principal $z$ axis. These findings demonstrate that the spatial and temporal geometry of orthogonal laser fields provides an additional degree of freedom for controlling ultrafast electron-nuclear dynamics.

physics.atom-ph↗

arXiv2026

Infinite-time surface flux for full-dimensional three-body breakup dynamics

We derive an infinite-time surface-flux formulation for full-dimensional three-body breakup dynamics in intense laser fields. The method is designed as a post-pulse extension of time-dependent surface flux (tSurff) calculations for systems with two asymptotic fragments, with helium double ionization and dissociative ionization of $\hydroplus$ as representative applications. Standard tSurff calculations avoid projection on very large boxes, but the spectra still contain a field-free tail after the laser pulse; converging this tail by direct propagation can be expensive for slow particles, narrow resonances, and long-range Coulomb channels. Here the post-pulse time integrals are rewritten as resolvents of the field-free one-particle ionic Hamiltonians and of the full field-free three-body Hamiltonian. The resulting expressions separate the already available tSurff amplitudes from stationary correction terms that can be evaluated from saved wave functions in the inner and single-ionization regions. The formulation gives a common theoretical structure for electron-electron breakup in helium and electron-nuclear breakup in $\hydroplus$, and it is compatible with the spectral decompositions and MPI-parallel workflow of the tRecX framework. This provides a practical route to tSurff+iSurff calculations of correlated three-body spectra without long post-pulse propagation and without solving a large complex linear system independently for every final momentum.

physics.atom-ph↗

arXiv2026

Towards a Universal Foundation Model for Protein Dynamics: A Multi-Chain Tree-Structured Framework with Transformer Propagators

Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves high-fidelity structural reconstruction and generalizes across diverse protein systems. Central to our approach is a hierarchical, tree-structured protein representation (TSCG) that maps Cartesian coordinates into a minimal set of interpretable collective variables. We extend this representation to accommodate multi-chain assemblies, demonstrating sub-angstrom precision in reconstructing full-atom structures from coarse-grained nodes. To model temporal evolution, we formulate protein dynamics as stochastic differential equations (SDEs), utilizing a Transformer-based architecture as a universal propagator. By representing collective variables as language-like sequences, our model transcends the limitations of protein-specific networks, generalizing to arbitrary sequence lengths and multi-chain configurations. The framework achieves an acceleration of over 10,000 to 20,000 times compared to traditional MD, generating microsecond-long trajectories within minutes. Our results show that the generated trajectories maintain statistical consistency with all-atom MD in RMSD profiles and structural ensembles. This universal model provides a salable solution for high-throughput protein simulation, offering a significant leap toward a foundation model for molecular dynamics.

physics.atom-ph↗

arXiv2026

The 1/3 Geometric Constant: Scale Invariance and the Origin of 'Missing Energy' in 3D Quantum Fragmentation

We report the discovery of a universal geometric constraint on the detection of kinetic energy release (KER) in three-dimensional quantum fragmentation. By analyzing the dissociation of localized wavepackets, we demonstrate that the $4πr^2$ radial volume element acts as a topological filter that inherently masks a significant portion of a system's energy budget, imposing a fundamental peak-to-mean bound of $R_E < 0.5$. We introduce an invariant scaling law, $α= MQ/ζ$, and prove that the resulting energy detection ratio is scale-invariant across twelve orders of magnitude, bridging attosecond molecular science and nuclear physics. We identify a universal \textbf{geometric landmark} at $R_E \approx 0.33$, which precisely replicates the 7~eV discrepancy in $H_2^+$ fragmentation. Furthermore, we show that the population of excited-state manifolds and the increase in nuclear localization ($ζ$) provide a definitive geometric mechanism for the \textbf{spectral broadening} observed across atomic and subatomic scales. Remarkably, the spectral morphology derived from our scaling law aligns with the universal 1/3 energy landmark of historical beta decay, while the high-mass limit naturally accounts for the sharpening of alpha spectra. Our results suggest that ``missing energy'' is often a topological artifact of 3D geometry rather than an exclusive signature of undetected particles. This work establishes a universal master curve for energy reconstruction and identifies a \textbf{``detection crisis''} in highly localized systems, where the true interaction energy becomes effectively invisible to peak-centric calorimetry.

physics.atom-ph↗

arXiv2026

Resonant Coupling Between Electromagnetic Waves and Protein Conformational Dynamics Revealed by Molecular Dynamics Simulations

The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can modulate protein conformation through resonant coupling with intrinsic protein dynamics. Molecular dynamics simulations were employed to characterize spontaneous conformational fluctuations in the absence of external fields, and a tiered screening strategy combined with fast Fourier transform analysis was used to identify dominant intrinsic frequencies associated with periodically fluctuating non-covalent atom or residue pairs. Oscillating external electric fields were subsequently applied at resonant and off-resonant frequencies to evaluate conformational responses across diverse protein systems. The results demonstrate that resonant excitation induces significantly enhanced backbone conformational deviations compared to off-resonant conditions, with the effect becoming more pronounced in structurally flexible and multichain proteins. These findings provide atomistic evidence for frequency-specific resonance between electromagnetic fields and protein conformational dynamics, offering mechanistic insight into frequency-dependent electromagnetic effects and a computational framework for electromagnetic wave-based modulation of protein function.

physics.chem-ph↗

arXiv2025

On projection mappings and the gradient projection method on hyperbolic space forms

This paper presents several new properties of the intrinsic $κ$-projection into $κ$-hyperbolically convex sets of $κ$-hyperbolic space forms, along with closed-form formulas for the intrinsic $κ$-projection into specific $κ$-hyperbolically convex sets. It also discusses the relationship between the intrinsic $κ$-projection, the Euclidean orthogonal projection, and the Lorentz projection. These properties lay the groundwork for analyzing the gradient projection method and hold importance in their own right. Additionally, new properties of the gradient projection method to solve constrained optimization problems in $κ$-hyperbolic space forms are established, considering both constant and backtracking step sizes in the analysis. It is shown that every accumulation point of the sequence generated by the method for both step sizes is a stationary point for the given problem. Additionally, an iteration complexity bound is provided that upper bounds the number of iterations needed to achieve a suitable measure of stationarity for both step sizes. Finally, the properties of the constrained Fermat-Weber problem are explored, demonstrating that the sequence generated by the gradient projection method converges to its unique solution. Numerical experiments on solving the Fermat-Weber problem are presented, illustrating the theoretical findings and demonstrating the effectiveness of the proposed methods.

math.OC↗

arXiv2024

A unified framework for coarse grained molecular dynamics of proteins with high-fidelity reconstruction

Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a hierarchical protein representation, our model accurately reconstructs high-resolution protein structures, with sub-angstrom precision achieved for a 168-amino acid protein. We combine this coarse-grained model with a deep learning framework based on stochastic differential equations (SDEs). A neural network is trained to model the drift force, while a RealNVP-based noise generator approximates the stochastic component. This approach enables a significant speedup of over 20,000 times compared to traditional MD, allowing for the generation of microsecond-long trajectories within a few minutes and providing valuable insights into protein behavior. Our method demonstrates high accuracy, achieving sub-angstrom reconstruction for short (25 ns) trajectories and maintaining statistical consistency across multiple independent simulations.

physics.chem-ph↗

arXiv2022

Convexity of sets and quadratic functions on the hyperbolic space

In this paper some concepts of convex analysis on hyperbolic space are studied. We first study properties of the intrinsic distance, for instance, we present the spectral decomposition of its Hessian. Next, we study the concept of convex sets and the intrinsic projection onto these sets. We also study the concept of convex functions and present first and second order characterizations of these functions, as well as some optimization concepts related to them. An extensive study of the hyperbolically convex quadratic functions is also presented.

math.OC↗

arXiv2021

A quantum simulation of dissociative ionization of $H_2^+$ in full dimensionality with time dependent surface flux method

The dissociative ionization of $H_2^+$ in a linearly polarized, 400 nm laser pulse is simulated by solving a three-particle time-dependent Schrödinger equation in full dimensionality without using any data from quantum chemistry computation. The joint energy spectrum (JES) is computed using a time-dependent surface flux (tSurff) method, the details of which are given. The calculated ground energy is -0.597 atomic units and internuclear distance is 1.997 atomic units if the kinetic energy term of protons is excluded, consistent with the reported precise values from quantum chemistry computation. If the kinetic term of the protons is included, the ground energy is -0.592 atomic units with an internuclear distance 2.05 atomic units. Energy sharing is observed in JES and we find peak of the JES with respect to nuclear kinetic energy release (KER) is within $2\sim4$ eV, which is different from the previous two dimensional computations (over 10 eV), but is close to the reported experimental values. The projected energy distribution on azimuth angles shows that the electron and the protons tend to dissociate in the direction of polarization of the laser pulse.

physics.atom-ph↗

arXiv2021

Theoretical investigation of the Freeman resonance in the dissociative ionization of $H_2+$

The dissociative ionization of $H_2^+$ in linearly polarized, 400 nm laser pulses is simulated by solving a three-particle time-dependent Schrödinger equation in full dimensionality. The joint energy spectra (JES) are computed for $\cos^8$ and flat-top envelopes using the time-dependent surface flux (tSurff) methods. In JES, the energy sharing $n$ photon energies $ω$ of nuclear kinetic energy release (KER) $E_N$ and electronic KER $E_e$ are well represented by $E_N+E_e=nω-U_p+E_0$ for $\cos^8$ pulses, but satisfy $E_N+E_e=nω+E_0$ for flat-top envelope, exposing a deviation of the ponderomotive energy $U_p$, which has been observed in experiments, where $E_0$ is the ground energy of $H_2^+$. The analysis of the wavefunction for electrons and protons after the pulse are presented, where we find $U_p$ is absorbed by the Freeman resonances between two excited ungerade states.

physics.atom-ph↗

arXiv2019

Electron double-emission spectra for Helium atoms in intense 400 nm laser pulses

Double photoelectron emission from He atoms by intense laser pulses with a wave length of $394.5\,nm$ is computed for intensities $3.5 - 9.2\times 10^{14}W/cm^2$. Joint momentum distributions confirm the characteristics seen in classical trajectory calculations. The pronounced transition from back-to-back to side-by-side emission with increasing intensity, the $He^{++}/He^+$ ratios, and a modulation of joint energy spectra agree well with a recent experiment [Henrichs et al., PRA 98, 43405 (2018)], if one admits an increase of experimental intensities by a factor $\sim 2$. We find that Freeman resonances enhance anti-correlated emission, we identify the signature of electron repulsion in joint angular distributions, and we interpret the modulation of joint energy spectra as a signature of multiple recollsions.

physics.atom-ph↗