Related papers: Viral Lattice Theory: A Biophysical Model for Viri…
We develop a comprehensive theoretical biophysics model grounded in a path integral perspective and an m-sectorial open-system framework, to describe complex, damped viral phonon dynamics in resource limited and noise driven environments.…
A vibrational model of transport properties of dense fluids assumes that solid-like oscillations of atoms around their temporary equilibrium positions dominate the dynamical picture. The temporary equilibrium positions of atoms do not form…
Emergent lattices at mesoscopic length scales have evoked interest in several recent contexts, e.g., in crystalline arrangements of skyrmions. It is a challenging task to determine their collective excitations as the unit cells are large…
Lattice vibration modes are collective excitations in periodic arrays of atoms or molecules. These modes determine novel transport properties in solid crystals. Analogously, in periodical arrangements of magnetic vortex-state disks,…
A communication protocol is proposed in which quantum state transfer is mediated by a vibrational exciton. We consider two distant molecular groups grafted on the sides of a lattice. These groups behave as two quantum computers where the…
Paramagnetic molecules can show long spin-coherence times, which make them good candidates as quantum bits. Reducing the efficiency of the spin-phonon interaction is the primary challenge towards achieving long coherence times over a wide…
We consider a quantum particle, moving on a lattice with a tight-binding Hamiltonian, which is subjected to measurements to detect it's arrival at a particular chosen set of sites. The projective measurements are made at regular time…
The lattice Boltzmann equation (LBE), rooted in kinetic theory, provides a powerful framework for capturing complex flow behaviour by describing the evolution of single-particle distribution functions (PDFs). Despite its success, solving…
A general phenomenological theory describing dynamics of Josephson vortices coupled to wide class of linear waves in layered high-T$_c$ superconductors is developed. The theory is based on hydrodynamic long wave approximation and describes…
The influence of an electron-vibrational coupling on the laser control of electron transport through a molecular wire that is attached to several electronic leads is investigated. These molecular vibrational modes induce an effective…
I present the mathematical structure of classical phonon theory in a general form, which emphasizes the wave natures of phonons, and which can serve as a robust foundation for further development of the theory of strongly interacting…
We investigate the static and dynamical behavior of 1D interacting fermions in disordered Hubbard chains, contacted to semi-infinite leads. The chains are described via the repulsive Anderson-Hubbard Hamiltonian, using static and…
We study the stochastic spatial Lotka-Volterra (LV) model for predator-prey interaction subject to a periodically varying carrying capacity. The LV model with on-site lattice occupation restrictions that represent finite food resources for…
Modeling dispersed solid phases in fluids still represents a computational challenge when considering a small-scale coupling in wide systems, such as the atmosphere or industrial processes at high Reynolds numbers. A numerical method is…
Ion diffusion is important in a variety of applications, yet fundamental understanding of the diffusive process in solids is still missing, especially considering the interaction of lattice vibrations (phonons) and the mobile species. In…
Viruses display striking diversity in structure, transmission mode, immune interaction, and evolutionary behavior. Despite this diversity, viral strategies are not unconstrained. Here we present a unifying framework that treats viral…
Collective locomotion of swimming and flying animals is fascinating in terms of individual-level fluid mechanics and group-level structure and dynamics. Here we bridge and relate these scales through a model of formation flight that views…
Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Symmetry-determined nonlinear normal modes, which describe large-amplitude vibrations of diamond lattice, are studied by specific group-theoretical methods. For two of these modes, corresponding to vibrational state with and without…