arXiv subjects

Takahito Nakajima

Publications and source records attributed to Takahito Nakajima.

15 recordsLinked to original sources

arXiv2026

Band Structure Modulation of ZrO2 Nanoparticles for Control of CO Adsorption Properties: A Combined Density Functional Theory - Density Functional Tight Binding Study

We present a combined density functional theory (DFT) and density functional tight binding (DFTB) study of zirconia (ZrO2) nanoparticles of experimentally relevant sizes of several nanometers and their interactions with the CO molecule. A hybrid DFTB - Force Field (DFTB-FF) framework is developed, whereby band structure calculations rely on an existing Slater-Koster framework, while the accuracy of structural optimization and adsorption properties is controlled by the introduction of classical long-range interatomic potentials into DFTB instead of the traditional repulsive potentials. Additionally, coordination-dependent Zr-C potentials are introduced to account for the distinct local chemical environments of bulk-like facet sites and under-coordinated tip and edge sites, thereby improving the description of CO adsorption. This hybrid DFTB-FF approach substantially improves the robustness of geometry optimization and provides a practical strategy for extending the applicability of DFTB to complex oxide nanostructures. The calculations reveal that termination stoichiometry can be used to engineer intrinsic, p-type, or n-type electronic structures and thereby tune the adsorption activity of zirconia nanoparticles. While stoichiometric nanoparticles do not activate the C-O bond, low-coordinated sites in Zr-rich (n-type) nanoparticles exhibit chemisorption accompanied by charge donation into a CO antibonding LUMO-derived orbital, resulting in C-O bond activation. These results demonstrate that stoichiometry-controlled electronic structure and under-coordinated surface sites introduced by nanostructuring play a key role in governing the adsorption strength and reactivity of zirconia nanoparticles.

cond-mat.mtrl-sci↗

arXiv2026

MedBeads: An AI-Native Clinical Context Graph Built from Immutable Beads and Reconstructable Clinical Links

Generative AI can encode substantial medical knowledge, but patient-specific answers remain constrained by the context supplied at inference time. Electronic health records and FHIR support documentation and interoperability, but they do not by themselves define the complete, current, and auditable context a model should receive. Similarity-based retrieval can find related text, but it neither guarantees collection of clinically connected records nor makes omissions explicit. We introduce MedBeads, an AI-facing clinical record substrate that assembles a declared closure of longitudinal patient information before generation. A Bead is an immutable clinical or knowledge object identified by SHA-256 over canonical content and stored as an append-only frame in a patient-scoped Pod. Structural parent edges form a patient-rooted Merkle DAG. Typed clinical links occupy a separate, reconstructable interpretation layer derived from signed, versioned knowledge rules; they can be recomputed when knowledge changes without rewriting clinical facts. Retrieval follows authorized structural and clinical edges, resolves amendments and retractions, and reports policy or token truncation. An open-source Go implementation uses append-only Pods and reconstructable SQLite projections. File-based conversion of 1,135 synthetic Synthea FHIR bundles produced approximately one million Beads and demonstrated deterministic clinical-link derivation and interpretation-layer reconstruction. These engineering results establish feasibility and reproducibility, not reduced hallucination or improved clinical outcomes. MedBeads reframes grounding as a data-structure problem by delivering a policy-bounded, provenance-bearing clinical subgraph rather than an opaque list of similar fragments.

cs.AI↗

arXiv2026

A Scalable Diagonalization Framework for Tensor-Product Bitstring Selected Configuration Interaction

Selected configuration interaction (SCI) methods are effective for treating strongly correlated electronic systems, yet their scalability has long been limited by implementations that replicate the configuration interaction (CI) vector across processes, leading to severe memory bottlenecks. Here, we present a fully distributed diagonalization framework tailored for extremely large selected determinant spaces, directly addressing this major scalability bottleneck of modern SCI methods. The method is grounded in a tensor-product bitstring (TPB) representation, in which determinants are organized through a TPB structure constructed from selected alpha- and beta-bitstrings, and is referred to as tensor-product bitstring SCI (TBSCI). An efficient TBSCI eigensolver is developed based on a novel bitstring-based Hamiltonian evaluation algorithm together with a suite of MPI communication strategies designed to improve parallel efficiency. Large-scale full configuration interaction (FCI) benchmarks, employed as communication-intensive stress tests, demonstrate that the implemented TBSCI eigensolver continues to reduce the wall time for distributed diagonalization of 2.6 trillion determinants, reaching 54,000 nodes (more than 2.5 million cores) on supercomputer Fugaku. Beyond scalability, we investigate the structural compactness of the TPB representation and show that selecting alpha- and beta-bitstrings according to their collective weights in a reference SCI wavefunction yields TPB-based wavefunctions approaching the FCI limit while using only a small fraction of determinants. These results establish TBSCI as a scalable SCI methodology and provide evidence for the intrinsic compactness of the TPB representation.

physics.chem-ph↗

arXiv2026

Quantum-HPC hybrid computation of biomolecular excited-state energies

We develop a workflow within the ONIOM framework and demonstrate it on the hybrid computing system consisting of the supercomputer Fugaku and the Quantinuum Reimei trapped-ion quantum computer. This hybrid platform extends the layered approach for biomolecular chemical reactions to accurately treat the active site, such as a protein, and the large and often weakly correlated molecular environment. Our result marks a significant milestone in enabling scalable and accurate simulation of complex biomolecular reactions

quant-ph↗

arXiv2024

Reducing Numerical Precision Requirements in Quantum Chemistry Calculations

The abundant demand for deep learning compute resources has created a renaissance in low precision hardware. Going forward, it will be essential for simulation software to run on this new generation of machines without sacrificing scientific fidelity. In this paper, we examine the precision requirements of a representative kernel from quantum chemistry calculations: calculation of the single particle density matrix from a given mean field Hamiltonian (i.e. Hartree-Fock or Density Functional Theory) represented in an LCAO basis. We find that double precision affords an unnecessarily high level of precision, leading to optimization opportunities. We show how an approximation built from an error-free matrix multiplication transformation can be used to potentially accelerate this kernel on future hardware. Our results provide a road map for adapting quantum chemistry software for the next generation of High Performance Computing platforms.

physics.chem-ph↗

arXiv2023

Exploratory Data Science on Supercomputers for Quantum Mechanical Calculations

Literate programming - the bringing together of program code and natural language narratives - has become a ubiquitous approach in the realm of data science. This methodology is appealing as well for the domain of Density Functional Theory (DFT) calculations, particularly for interactively developing new methodologies and workflows. However, effective use of literate programming is hampered by old programming paradigms and the difficulties associated with using High Performance Computing (HPC) resources. Here we present two Python libraries that aim to remove these hurdles. First, we describe the PyBigDFT library, which can be used to setup materials or molecular systems and provides high-level access to the wavelet based BigDFT code. We then present the related remotemanager library, which is able to serialize and execute arbitrary Python functions on remote supercomputers. We show how together these libraries enable transparent access to HPC based DFT calculations and can serve as building blocks for rapid prototyping and data exploration.

physics.chem-ph↗

arXiv2023

Complexity Reduction in Density Functional Theory: Locality in Space and Energy

We present recent developments of the NTChem program for performing large scale hybrid Density Functional Theory calculations on the supercomputer Fugaku. We combine these developments with our recently proposed Complexity Reduction Framework to assess the impact of basis set and functional choice on its measures of fragment quality and interaction. We further exploit the all electron representation to study system fragmentation in various energy envelopes. Building off this analysis, we propose two algorithms for computing the orbital energies of the Kohn-Sham Hamiltonian. We demonstrate these algorithms can efficiently be applied to systems composed of thousands of atoms and as an analysis tool that reveals the origin of spectral properties.

physics.chem-ph↗

arXiv2022

Probing Disorder in 2CzPN using Core and Valence States

Molecules which exhibit thermally activated delayed fluorescence (TADF) show great promise for use in efficient, environmentally-friendly OLEDs, and thus the design of new TADF emitters is an active area of research. However, when used in devices, they are typically in the form of disordered thin films, where both the external molecular environment and thermally-induced internal variations in parameters such as the torsion angle can strongly influence their electronic structure. In this work, we use density functional theory and X-ray photoelectron spectroscopy to investigate the impact of disorder on both core and valence states in the TADF emitter 2CzPN. By simulating gas phase molecules displaying varying levels of disorder, we assess the relative sensitivity of the different states to factors such as varying torsion angle. The theoretical results for both core and valence states show good agreement with experiment, thereby also highlighting the advantages of our approach for interpreting experimental spectra of large aromatic molecules, which are too complex to interpret based solely on experimental data.

physics.chem-ph↗

arXiv2020

Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding

With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments, and quantify inter-fragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems, and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.

physics.chem-ph↗

arXiv2020

Stereo-specific internally entangled roaming mechanism in the reaction of unstable B5 cluster with H

A new type of, called stereo-specific entangled, roaming mechanism is presented in the reaction of structurally unstable B5 cluster with the hydrogen atom, by using the direct ab initio trajectory calculation with a practical level of DFT method using the rang-separated functional. In this mechanism, the light moiety, i.e. H roams around far from the B5 cluster caused by a stereo-specific energy transfer of translational energy to the cluster vibrational energy through the direct coupling due to the large amplitude motion of the unstable B5 cluster. We confirmed by the comparative computation that a clear change occur from the roaming trajectory to the repulsive trajectory, when we froze the vibrational motion of the B5 cluster. This drastic change of the trajectory due to the change between the structurally unstable B5 cluster and the frozen B5 cluster revealed the importance of kinematic energy transfer resulted in the soft-landing-like hydrogen absorption which manifested the present stereo-specific entangled roaming mechanism. The trajectory calculation revealed that the present new type of roaming mechanism is very sensitive to the azimuthal angle of the H atom attack, especially to the bisection of the B-B bond of the B5 cluster, where the energy flow from relative kinetic energy to the vibrational energy of the cluster efficiently takes place through the roaming trajectory driven due to the structural fluctuation of the B5 cluster.

physics.chem-ph↗

arXiv2019

Electron dynamics method using a locally projected group diabatic Fock matrix for molecules and aggregates

We propose a method using reduced size of Hilbert space to describe an electron dynamics in molecule and aggregate based on our previous theoretical scheme [ T. Yonehara and T. Nakajima, J. Chem. Phys. \textbf{147}, 074110 (2017) ]. The real-time time-dependent density functional theory is combined with newly introduced projected group diabatic Fock matrix. First, this projection method is applied to a test donor--acceptor dimer, namely, a naphthalene--tetracyanoethylene with and without initial local excitations and light fields. Secondly, we calculate an absorption spectrum of five-unit-polythiophene monomer. The importance of feedback of instantaneous density to Fock matrix is also clarified. In all cases, half of the orbitals were safely reduced without loss of accuracy in descriptions of properties. The present scheme provides one possible way to investigate and analyze a complex excited electron dynamics in molecular aggregates within a moderate computational cost.

physics.chem-ph↗

arXiv2019

Required number of states increases only moderately with the problem size for antisymmetrized geminal powers

We propose an algorithm to obtain the ground-state energy of a many-electron system using the variational wave function of a linear combination of antisymmetrized geminal powers. We optimized this algorithm to obtain the energy and the other parameters of a many-electron system. Also we clarified the bottleneck of the total calculation in the tensor contraction and successfully reduced the computational time. As a result, we can use an extended number of geminal states to obtain the ground state of the water molecule and Hubbard models. The result for the water molecule with the Dunning double-zeta basis is of the sub-milihartree order above the energy of exact diagonalization. Further, we observe that the result for the one-dimensional Hubbard model with 14 sites shows good tendency to capture the right ground state and that for the two-dimensional Hubbard model still lacks some part of the energy reflecting the large size of the Hilbert space. We conclude that the required number of terms for geminal states for sufficiently accurate energy is only moderately affected by the problem size. We further show other technical details for the numerical algorithms of geminal states in the variation process. It is expected that with the use of more extended computing resources and larger sizes of electronic systems, our algorithm can provide improved results.

physics.chem-ph↗

arXiv2018

Antisymmetrized Geminal Powers with Larger Chemical Basis Sets

In previous research, we tested the wave function format of a linear combination of several antisymmetrized geminal power states. A numerical problem in the geminal matrices was noted, which made the total energies of electronic systems with large numbers of electrons unstable. The underlying cause was found to be the large cancellation term in the geminal power series. We have obtained a new format to resolve this problem for the case of total energies and partly for the first-order derivatives within the antisymmetrized geminal power states. By using this new formalism, we have calculated the ground state energies for several electronic systems, including the usage of a larger chemical basis set. The results are, in some cases, very close to the exact result, especially for one-dimensional Hubbard systems. Our result for a water molecule with the Dunning Zeta basis set is better than the CISD energy and approaches the CCSD energy.

physics.chem-ph↗

arXiv2017

Efficient Computation of Sparse Matrix Functions for Large-Scale Electronic Structure Calculations: The CheSS Library

We present CheSS, the "Chebyshev Sparse Solvers" library, which has been designed to solve typical problems arising in large-scale electronic structure calculations using localized basis sets. The library is based on a flexible and efficient expansion in terms of Chebyshev polynomials and presently features the calculation of the density matrix, the calculation of matrix powers for arbitrary powers, and the extraction of eigenvalues in a selected interval. CheSS is able to exploit the sparsity of the matrices and scales linearly with respect to the number of nonzero entries, making it well-suited for large-scale calculations. The approach is particularly adapted for setups leading to small spectral widths of the involved matrices and outperforms alternative methods in this regime. By coupling CheSS to the DFT code BigDFT, we show that such a favorable setup is indeed possible in practice. In addition, the approach based on Chebyshev polynomials can be massively parallelized, and CheSS exhibits excellent scaling up to thousands of cores even for relatively small matrix sizes.

physics.chem-ph↗

arXiv2017

A quantum dynamics method for excited electrons in molecular aggregate system using a group diabatic Fock matrix

We introduce a practical calculation scheme for the description of excited electron dynamics in molecular aggregated systems within a locally group diabatic Fock representation. This scheme makes it easy to analyze the interacting time-dependent excitations of local sites in complex systems. In addition, light-electron couplings are considered. The present scheme is intended for investigations on the migration dynamics of excited electrons in light-energy conversion systems. The scheme was applied to two systems: a naphthalene(NPTL)-tetracyanoethylene(TCNE) dimer and a 20-mer circle of ethylene molecules. Through local group analyses of the dynamical electrons, we obtained an intuitive understanding of the electron transfers between the monomers.

physics.chem-ph↗