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Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multi-referenced) electrons. We use a low-cost approximate solution of…
We study the tensor-optimized antisymmetrized molecular dynamics (TOAMD) as a successive variational method in many-body systems with strong interaction for nuclei. In TOAMD, the correlation functions for the tensor force and the…
Characteristic Mode analysis is a widely used technique in antenna design, providing insight into the fundamental electromagnetic properties of radiating structures. In this paper, we establish fundamental bounds on the slope of…
Analytical formulas for the excitation energies as well as for the electric quadrupole reduced transition probabilities in the ground, beta and gamma bands were derived within the coherent state model for the near vibrational and well…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
Polymer self-consistent field theory techniques are used to find radial electron densities and total binding energies for isolated atoms. Quantum particles are modelled as Gaussian threads with ring-polymer architecture in a four…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
Amplitude-modulation atomic force microscopy enables observation of fragile molecules at the nanometer scale. To shorten measurement times and capture dynamic molecules, increasing the frame rate is essential. Traditionally, maximum frame…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Proteinoids are solidified gels made from poly(amino acids) based polymers that exhibit oscillatory electrical activity. It has been proposed that proteinoids are capable of performing analog computing as their electrical activity can be…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the…
The instantaneous normal modes corresponding to base pair vibrations (radial modes) and twist angle fluctuations (angular modes) of a DNA molecule model at ambient temperature are theoretically investigated. Due to thermal disorder, normal…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
A new method describing nuclear rotational motion microscopically is proposed. We extract the rotational Hamiltonian by introducing the intrinsic pair modes which commute with the rotational mode. Thereby the rotational mode is not treated…
Decomposition of atomic motion into individual normal modes has led to remarkable success in microscopically understanding thermal properties and thermodynamics in simple solids. We start this chapter with an example of decomposing atomic…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…