Related papers: Modeling truncated hemoglobin vibrational dynamics
We propose a Truncated Gaussian Basis Approach (TGBA) for simulating the dynamics of quantum many-body systems. The approach constructs an effective Hamiltonian within a reduced subspace, spanned by fermionic Gaussian states, and…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale…
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…
We consider the Bayesian approach to the linear Gaussian inference problem of inferring the initial condition of a linear dynamical system from noisy output measurements taken after the initial time. In practical applications, the large…
Recent experimental evidence for collective protein vibrations in the terahertz (THz) domain indicates that energy in biomolecular systems can self-organize in an orderly manner, as anticipated by Fr\"ohlich's theory of condensates within a…
We study the quantum dynamics of the Bose-Hubbard model on a ladder formed by two rings coupled by tunneling effect. By implementing the Bogoliubov approximation scheme, we prove that, despite the presence of the inter-ring coupling term,…
Inspired by holographic Wilsonian renormalization, we consider coarse graining a quantum system divided between short distance and long distance degrees of freedom, coupled via the Hamiltonian. Observations using purely long distance…
We present a framework for simulating the open dynamics of spin-boson systems by combining variational non-Gaussian states with a quantum trajectories approach. We apply this method to a generic spin-boson Hamiltonian that has both…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
We study numerically the thermalisation and temporal evolution of the reduced density matrix for a two-site subsystem of a fermionic Hubbard model prepared far from equilibrium at a definite energy. Even for very small systems near quantum…
We show how to evaluate mobility profiles, characterizing the transport of confined fluids under a perturbation, from equilibrium molecular simulations. The correlation functions derived with the Green-Kubo formalism are difficult to sample…
We discuss stochastic phase-space methods within the truncated Wigner approximation and show explicitly that they can be used to solve non-equilibrium dynamics of bosonic atoms in one-dimensional traps. We consider systems both with and…
We study the non-equilibrium dynamics of the quantum sine-Gordon model describing a pair of Josephson-coupled one-dimensional bosonic quasi-condensates. Motivated by experimentally accessible quench procedures where the zero mode of the…
We apply a Gaussian variational approximation to model reduction in large biochemical networks of unary and binary reactions. We focus on a small subset of variables (subnetwork) of interest, e.g. because they are accessible experimentally,…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation (M. Tirion, PRL 77, 1905 (1996)) that characterized the slow modes associated with protein data bank…
We investigate the weak excitations of a system made up of two condensates trapped in a Bose-Hubbard ring and coupled by an interspecies repulsive interaction. Our approach, based on the Bogoliubov approximation scheme, shows that one can…
\gamma-softness in atomic nuclei is investigated in the framework of energy density functionals. By mapping constrained microscopic energy surfaces for a set of representative non-axial medium-heavy and heavy nuclei to a Hamiltonian of the…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…