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A realistic continuous-time dynamics for fiber bundles is introduced and studied both analytically and numerically. The equation of motion reproduces known stationary-state results in the deterministic limit while the system under…
Nuclear deformation effects are theoretically investigated in terms of deformation corrections of the electronic binding and transition energies, $g$ factor, and hyperfine splitting constant. By solving the Dirac equation twice, with the…
This is an archival document; the work contains theoretical development to be used in new publications and to stimulate further development. Here, we develop a statistical mechanical treatment of a braid formed of two molecules subject to…
We present a consistent analysis of linear spectroscopy for arrays of nearest neighbor dipole-coupled two-level molecules that reveals distinct signatures of weak and strong coupling regimes separated for infinite size arrays by a quantum…
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA…
A particular difficulty in studying many-body interactions in a solid is the absence of an experimental technique that can directly probe their key characteristics. We show that 2D Fourier spectroscopy provides an efficient tool for the…
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
The pervasive phenomenon of friction has been studied at the nanoscale by controlled manipulation of single atoms and molecules, which permitted a precise determination of the static friction force necessary to initiate motion. However,…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Friction is one of the fundamental issues in physics, mechanics and material science with lots of practical applications. However, the understanding of macroscopic friction phenomena from microscopic aspect is still on the way. In this…
High-energy nucleus-nucleus collisions are studied in multi-chain model with successive collision. Analytic forms for single-particle distribution are derived.
Stochasticity is a defining feature of the pairwise forces governing interactions in biological systems-from molecular motors to cell-cell adhesion-yet its consequences on large-scale dynamics remain poorly understood. Here, we show that…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
We consider the rupture dynamics of a homopolymer chain pulled at one end at a constant loading rate r. Compared to single bond breaking, the existence of the chain introduces two new aspects into rupture dynamics: the non-Markovian aspect…
The dynamical systems found in Nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and…
Including information from additional spectral bands (e.g., near-infrared) can improve deep learning model performance for many vision-oriented tasks. There are many possible ways to incorporate this additional information into a deep…
The concept of chemical bonding is a crucial aspect of chemistry that aids in understanding the complexity and reactivity of molecules and materials. However, the interpretation of chemical bonds can be hindered by the choice of the…