Related papers: Modeling truncated hemoglobin vibrational dynamics
Gaussian graphical models (GGMs) are widely used for statistical modeling, because of ease of inference and the ubiquitous use of the normal distribution in practical approximations. However, they are also known for their limited modeling…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Gaussian distribution is commonly used as a good approximation to study the trapped one-component Bose-condensed atoms with relatively small nonlinear effect. It is not adequate in dealing with the one-component system of large nonlinear…
We present a method to describe driven-dissipative multi-mode systems by considering a truncated hierarchy of equations for the correlation functions. We consider two hierarchy truncation schemes with a global cutoff on the correlation…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Realistic description of patient-specific mechanical properties of clotting dynamics presents a major challenge. Available patient-specific data falls short of robustly characterizing myriads of complex dynamic interactions that happen…
We numerically examine slow and hierarchical relaxation dynamics of interacting bosons described by a tilted two-band Bose-Hubbard model. The system is found to exhibit signatures of quantum chaos within the spectrum and the validity of the…
We report on the out-of-equilibrium dynamics of a Bose-Einstein condensate (BEC) placed in an optical lattice whose phase is suddenly modulated. The frequency and the amplitude of modulation are chosen to ensure a negative renormalized…
We apply the framework of non-equilibrium quantum thermodynamics to the physics of quenched small-sized bosonic quantum gases in a one-dimensional harmonic trap. We show that dynamical orthogonality can occur in these few-body systems with…
Finite systems of bosons and/or fermions described by the Hubbard model can be realized using ultracold atoms confined in optical lattices. The ground states of these systems often exhibit a coexistence of compressible superfluid and…
In this work, we analyze the Born, Bogoliubov, Green, Kirkwood and Yvon (BBGKY) hierarchy of equations for describing the full time-evolution of a many-body fermionic system in terms of its reduced density matrices (at all orders). We…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
We study the equilibrium and near-equilibrium properties of a holographic five-dimensional model consisting of Einstein gravity coupled to a scalar field with a non-trivial potential. The dual four-dimensional gauge theory is not conformal…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
Analogue models for gravity intend to provide a framework where matter and gravity, as well as their intertwined dynamics, emerge from degrees of freedom that have a priori nothing to do with what we call gravity or matter. Bose Einstein…
We study dissipation in a small quantum system coupled to an environment held in thermodynamic equilibrium. The relaxation dynamics of a system subject to an abrupt quench in the parameters of the underlying Hamiltonian is investigated…
We study the dynamics of a two-component Bose-Einstein condensate (BEC) of $^{174}$Yb atoms coherently driven on a narrow optical transition. The excitation transfers the BEC to a superposition of states with different internal and momentum…
In this work, which is based on our previously derived theoretical framework [1], we apply the truncated Born-Bogoliubov-Green-Kirkwood-Yvon (BBGKY) hierarchy for ultracold bosonic systems with a fixed number of particles to two…
In this paper, considering a braided continuum soft-robot, whose radial deformation is constrained but elongation is assumed, a quasi-Lagrangian model is proposed that meets the Lagrangian models properties, including a well-posed input…