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Koji Ando

Publications and source records attributed to Koji Ando.

15 recordsLinked to original sources

GPU implementation of mixed quantum-classical Liouville molecular dynamics without momentum jump

We implemented on GPU a mixed quantum-classical Liouville molecular dynamics simulation based on a momentum-jump-free theory. The trajectory spawning that was previously implemented on CPU for sampling enhancement was eliminated to avoid the overhead of thread divergence and dynamic memory allocation on the GPU. This achieved a speedup of an order of magnitude compared to the CPU computation with spawning, as well as a linear scaling with respect to the number of sampling trajectories.

physics.chem-ph

Predicting Generalization of AI Colonoscopy Models to Unseen Data

$\textbf{Background}$: Generalizability of AI colonoscopy algorithms is important for wider adoption in clinical practice. However, current techniques for evaluating performance on unseen data require expensive and time-intensive labels. $\textbf{Methods}$: We use a "Masked Siamese Network" (MSN) to identify novel phenomena in unseen data and predict polyp detector performance. MSN is trained to predict masked out regions of polyp images, without any labels. We test MSN's ability to be trained on data only from Israel and detect unseen techniques, narrow-band imaging (NBI) and chromendoscoy (CE), on colonoscopes from Japan (354 videos, 128 hours). We also test MSN's ability to predict performance of Computer Aided Detection (CADe) of polyps on colonoscopies from both countries, even though MSN is not trained on data from Japan. $\textbf{Results}$: MSN correctly identifies NBI and CE as less similar to Israel whitelight than Japan whitelight (bootstrapped z-test, |z| > 496, p < 10^-8 for both) using the label-free Frechet distance. MSN detects NBI with 99% accuracy, predicts CE better than our heuristic (90% vs 79% accuracy) despite being trained only on whitelight, and is the only method that is robust to noisy labels. MSN predicts CADe polyp detector performance on in-domain Israel and out-of-domain Japan colonoscopies (r=0.79, 0.37 respectively). With few examples of Japan detector performance to train on, MSN prediction of Japan performance improves (r=0.56). $\textbf{Conclusion}$: Our technique can identify distribution shifts in clinical data and can predict CADe detector performance on unseen data, without labels. Our self-supervised approach can aid in detecting when data in practice is different from training, such as between hospitals or data has meaningfully shifted from training. MSN has potential for application to medical image domains beyond colonoscopy.

eess.IV

Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol olfactory receptor

Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlfaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequent MD simulations the H-bond to Ser113 was formed in 2--4 ns. The lifetime of the H-bond was in the range of 1--20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the $α$-carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113 $\to$ Phe182 $\to$ (Leu259 or Tyr260) $\to$ Tyr291 induced by the ligand binding with a time scale of 4--6 ns.

physics.bio-ph

The unreasonable effectiveness of AI CADe polyp detectors to generalize to new countries

$\textbf{Background and aims}$: Artificial Intelligence (AI) Computer-Aided Detection (CADe) is commonly used for polyp detection, but data seen in clinical settings can differ from model training. Few studies evaluate how well CADe detectors perform on colonoscopies from countries not seen during training, and none are able to evaluate performance without collecting expensive and time-intensive labels. $\textbf{Methods}$: We trained a CADe polyp detector on Israeli colonoscopy videos (5004 videos, 1106 hours) and evaluated on Japanese videos (354 videos, 128 hours) by measuring the True Positive Rate (TPR) versus false alarms per minute (FAPM). We introduce a colonoscopy dissimilarity measure called "MAsked mediCal Embedding Distance" (MACE) to quantify differences between colonoscopies, without labels. We evaluated CADe on all Japan videos and on those with the highest MACE. $\textbf{Results}$: MACE correctly quantifies that narrow-band imaging (NBI) and chromoendoscopy (CE) frames are less similar to Israel data than Japan whitelight (bootstrapped z-test, |z| > 690, p < $10^{-8}$ for both). Despite differences in the data, CADe performance on Japan colonoscopies was non-inferior to Israel ones without additional training (TPR at 0.5 FAPM: 0.957 and 0.972 for Israel and Japan; TPR at 1.0 FAPM: 0.972 and 0.989 for Israel and Japan; superiority test t > 45.2, p < $10^{-8}$). Despite not being trained on NBI or CE, TPR on those subsets were non-inferior to Japan overall (non-inferiority test t > 47.3, p < $10^{-8}$, $δ$ = 1.5% for both). $\textbf{Conclusion}$: Differences that prevent CADe detectors from performing well in non-medical settings do not degrade the performance of our AI CADe polyp detector when applied to data from a new country. MACE can help medical AI models internationalize by identifying the most "dissimilar" data on which to evaluate models.

cs.LG

Potential energy surfaces for electron dynamics from a model of localized Gaussian wave packets with valence-bond spin-coupling: high-harmonic generation spectra from H and He atoms

Potential energy surfaces of electron dynamics (ePES) are constructed from a model of localized electron wave packets (eWP) with non-orthogonal valence-bond (VB) spin coupling and applied to quantum dynamics simulations of high harmonic generation (HHG) spectra of hydrogen and helium atoms induced by intense laser pulses. The dynamics of the single electron on the ePES is calculated by numerically solving the time-dependent Schrodinger equation. The results reasonably reproduce previous studies. The dynamics of the electron wave function, dipole moment and dipole acceleration were analyzed by comparing one- and two-dimensional calculations. It was found that the main part of the wave function remains within a few Bohrs of the nuclear position, while the part of the wave function that is several orders of magnitude smaller in probability density, which escapes the laser-induced potential barrier by quantum tunneling effect, mainly contributes to the HHG.

physics.chem-ph

Single-electron quantum dynamics in high-harmonic generation spectrum from LiH molecule: analysis of potential energy surfaces for electrons constructed from a model of localized Gaussian wave packets with valence-bond spin-coupling

High-harmonic generation (HHG) spectrum from a LiH molecule induced by an intense laser pulse is computed and analyzed with potential energy surfaces for electron motion (ePES) constructed from a model of localized electron wave packets (EWP) with valence-bond spin-coupling. The molecule has two valence ePES with binding energies of 0.39 hartree and 1.1 hartree. The HHG spectrum from an electron dynamics on the weaker bound valence ePES, virtually assigned to Li 2s, exhibits a dominant peak at the first harmonic without plateau and cut-off. This compares with the free electron spectrum under oscillating laser field and is comprehensive with the shape and depth of the ePES. The other valence ePES, assingned to H 1s, is deeper bound such that the overall profile of the wave function is well approximated by a Gaussian of the width comparable to the Li-H bond length. However, a small fraction, less than $10^{-3}$, of the probability density amplitude tunnels out from the bound potential with high wave number, and spreads over tens of nm's with parts recombining to the molecule due to the laser field oscillation. This minor portion of the electronic wave function is the major origin of the HHG extending up to 50 harmonic orders. Nonlinear dynamics within the potential well induced by the laser field oscillation also contributes to the HHG up to 30 harmonic orders.

physics.chem-ph

Potential energy surfaces for electron dynamics modeled by floating and breathing Gaussian wave packets with valence-bond spin-coupling: An analysis of high-harmonic generation spectrum

A model of localized electron wave packets (EWPs), floating and breathing Gaussians with non-orthogonal valence-bond spin-coupling, is applied to compute the high-harmonic generation (HHG) spectrum from a LiH molecule induced by an intense laser pulse. The characteristic features of the spectrum, a plateau up to 50 harmonic-order and a cut-off, agreed well with those from the previous time-dependent complete active-space self-consistent-field calculation [T. Sato and K. L. Ishikawa, Phys. Rev. A \textbf{91}, 023417 (2015)]. In contrast with the conventional molecular orbital picture in which the Li 2s and H 1s atomic orbitals are strongly mixed, the present calculation indicates that an incoherent sum of responses of single electrons reproduces the HHG spectrum, in which the contribution from H 1s electron dominates the plateau and cut-off, whereas the Li 2s electron contributes to the lower frequency response. The results are comprehensive in terms of the shapes of single-electron potential energy curves constructed from the localized EWP model.

physics.chem-ph

Localized electron wave packet description of chemical bond and excitation: Floating and breathing Gaussian with valence-bond coupling

A model of localized electron wave packets (WPs) with variable position and width (floating and breathing) that are spin-coupled as per the valence-bond theory is presented. It produces accurate potential energy curves of LiH in the ground singlet and triplet states. Quantization in a mean-field approximation of the motion of a WP that corresponds to the Li 2s electron generates semi-quantitative potential energy curves of low energy excited states. Real-time semiquantal dynamics of the WP induced by an intense laser pulse gives high-harmonic generation spectra that capture qualitative features of a higher-level wave function calculation.

physics.chem-ph

FMO3-LCMO study of electron transfer coupling matrix element and pathway: Application to hole transfer between two triptophanes through cis- and trans-polyproline-linker systems

The linear-combination of fragment molecular orbitals with three-body correction (FMO3-LCMO) is examined for electron transfer (ET) coupling matrix elements and ET pathway analysis, with application to hole transfer between two triptophanes bridged by cis- and trans-polyproline linker conformations. A projection to the minimal-valence-plus-core FMO space was found to give sufficient accuracy with significant reduction of computational cost while avoiding the problem of linear dependence of FMOs stemming from involvement of bond detached atoms.

physics.chem-ph

Charge-Transfer Matrix Elements by FMO-LCMO Approach: Hole Transfer in DNA with Parameter Tuned Range-Separated DFT

A scheme for computing charge-transfer matrix elements with the linear combination of fragment molecular orbitals and the 'nonempirically tuned range-separated' density functional is presented. It takes account of the self-consistent orbital relaxation induced by environmental Coulomb field and the exchange interaction in fragment pairs at low computational scaling along the system size. The accuracy was confirmed numerically on benchmark systems of imidazole and furane homo-dimer cations. Applications to hole transfers in DNA nucleobase pairs and in a $π$-stack adenine octomer highlight the effects of orbital relaxation.

physics.chem-ph

Electron transfer pathway analysis in bacterial photosynthetic reaction center

A new computational scheme to analyze electron transfer (ET) pathways in large biomolecules is presented with applications to ETs in bacterial photosynthetic reaction center. It consists of a linear combination of fragment molecular orbitals and an electron tunneling current analysis, which enables an efficient first-principles analysis of ET pathways in large biomolecules. The scheme has been applied to the ET from menaquinone to ubiquinone via nonheme iron complex in bacterial photosynthetic reaction center. It has revealed that not only the central Fe$^{2+}$ ion but also particular histidine ligands are involved in the ET pathways in such a way to mitigate perturbations that can be caused by metal ion substitution and depletion, which elucidates the experimentally observed insensitivity of the ET rate to these perturbations.

physics.chem-ph

A Corpuscular Picture of Electrons in Chemical Bond

We introduce a theory of chemical bond with a corpuscular picture of electrons. It employs a minimal set of localized electron wave packets with 'floating and breathing' degrees of freedom and the spin-coupling of non-orthogonal valence-bond theory. It accurately describes chemical bonds in ground and excited states of spin singlet and triplet, in a distinct manner from conventional theories, indicating potential for establishing a dynamical theory of electrons in chemical bonds.

physics.chem-ph

Mixed quantal-semiquantal dynamics with stochastic particles for backreaction

A mixed quantal-semiquantal theory is presented in which the semiquantal squeezed-state wave packet describes the heavy degrees of freedom. We first derive mean-field equations of motion from the time-dependent variational principle. Then, in order to take into account the interparticle correlation, in particular the 'quantum backreaction' beyond the mean-field approximation, we introduce the stochastic particle description for both the quantal and semiquantal parts. A numerical application on a model of O2 scattering from a Pt surface demonstrates that the proposed scheme gives correct asymptotic behavior of the scattering probability, with improvement over the mixed quantum-classical scheme with Bohmian particles, which is comprehended by comparing the Bohmian and the stochastic trajectories.

physics.chem-ph

Electrical spin injection in p-type Si using Fe/MgO contacts

We report the successful electrical creation of spin polarization in p-type Si at room temperature by using an epitaxial MgO(001) tunnel barrier and Fe(001) electrode. Reflection high-energy electron diffraction observations revealed that epitaxial Fe/MgO(001) tunnel contacts can be grown on a (2 x 1) reconstructed Si surface whereas tunnel contacts grown on the (1 x 1) Si surface were polycrystalline. Transmission electron microscopy images showed a more flat interface for the epitaxial Fe/MgO/Si compared to that of the polycrystalline structure. For the Fe/MgO/p-Si devices, the Hanle and inverted Hanle effects were clearly observed at 300 K by using a three-terminal configuration, proving that spin polarization can be induced in the Si at room temperature. Effective spin lifetimes deduced from the width of the Hanle curve were 95 +/- 6 ps and 143 +/- 10 ps for the samples with polycrystalline and epitaxial MgO tunnel contacts, respectively. The observed difference can be qualitatively explained by the local magnetic field induced by the larger roughness of the interface of the polycrystalline sample. The sample with epitaxial Fe/MgO tunnel contact showed higher magnitude of the spin accumulation with a nearly symmetric behavior with respect to the bias polarity whereas that of the polycrystalline MgO sample exhibited a quite asymmetric evolution. This might be attributed to the higher degree of spin polarization of the epitaxial Fe/MgO(001) tunnel contact, which acts as a spin filter. Our experimental results suggest that an epitaxial MgO barrier is beneficial for creating spins in Si.

cond-mat.mtrl-sci

Spin-transfer switching and thermal stability in an FePt/Au/FePt nanopillar prepared by alternate monatomic layer deposition

We fabricated a current-perpendicular-to-plane giant magnetoresistance (CPP-GMR) nanopillar with a 1-nm-thick FePt free layer having perpendicular anisotropy using the alternate monatomic layer deposition method. Nanopillars consisting of [Fe (1 monolayer (ML))/Pt (1 ML)]n (n: the number of the alternation period) ferromagnetic layers and an Au spacer layer showed spin-transfer induced switching at room temperature.

cond-mat.mtrl-sci