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A systematic and mechanistic connection between granular materials' macroscopic and grain level behaviors is developed for monodisperse systems of spherical elastic particles under die compaction. The Granular Micromechanics Approach (GMA)…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
Quantum geometrical molecular dynamics provides a quantum geometric picture for understanding reactive dynamics, especially excited-state conical intersection dynamics, and also a numerically exact method for strongly correlated…
Alignment of molecules through electric fields minimizes the averaging over orientations, e. g., in single particle imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor,…
This paper studies tensor-based Robust Principal Component Analysis (RPCA) using atomic-norm regularization. Given the superposition of a sparse and a low-rank tensor, we present conditions under which it is possible to exactly recover the…
We study the internal resonance, energy transfer, activation mechanism, and control of a model of DNA division via parametric resonance. While the system is robust to noise, this study shows that it is sensitive to specific fine scale modes…
A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
We have extended our analytically derived PDB-NMA formulation, ATMAN [1], to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3\AA\ resolution model of a small homodimer, ActVA-ORF6, consisting of…
The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…
Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…
We perform several numerical studies for our recently published adaptive compressive tomography scheme [D. Ahn et al. Phys. Rev. Lett. 122, 100404 (2019)], which significantly reduces the number of measurement settings to unambiguously…
A time-domain representation of chromatographic peak shapes is presented as an analytic expression designed for high computational efficiency, which can be used for direct time-domain peak fitting with parameters that represent physical…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
The protein backbone is described as a smooth curved and twisted line in three-dimensional (3D) space and characterized by its curvature $\kappa(s)$ and torsion $\tau(s)$ both expressed as a function of arc length s. It is shown that the…
The concepts of globule and random coil were developed to describe the phases of homopolymers and then used to characterize the denatured state of structured cytosolic proteins and intrinsically disordered proteins. Using multi-scale…
An effective model for protein structures is important for the study of protein geometry, which, to a large extent, determine the functions of proteins. There are a number of approaches for modelling; one might focus on the conformation of…
Characteristic modes of a spherical shell are found analytically as spherical harmonics normalized to radiate unitary power and to fulfill specific boundary conditions. The presented closed-form formulas lead to a proposal of precise…