Trajectory-based approaches to excited-state, nonadiabatic dynamics are promising simulation techniques to describe the response of complex molecular systems upon photo-excitation. They provide an approximate description of the coupled quantum dynamics of electrons and nuclei trying to access systems of growing complexity. The central question in the design of those approximations is a proper accounting of the coupling electron-nuclei and of the quantum features of the problem.

A dynamical system submitted to holonomic constraints is Hamiltonian only if considered in the reduced phase space of its generalized coordinates and momenta, which need to be defined ad hoc in each particular case. However, specially in molecular simulations, where the number of degrees of freedom is exceedingly high, the representation in generalized coordinates is completely unsuitable, although conceptually unavoidable, to provide a rigorous description of its evolution and statistical properties.

The time reversal invariance of classical dynamics is reconsidered in this paper with specific focus on its consequences for time correlation functions and associated properties such as transport coefficients. We show that, under fairly common assumptions on the interparticle potential, an isolated Hamiltonian system obeys more than one time reversal symmetry and that this entails non trivial consequences. Under an isotropic and homogeneous potential, in particular, eight valid time reversal operations exist.

Abstract

Background: Macrophages cover a major role in the immune system, being the most plastic cell yielding several key immune functions. Methods: Here we derived a minimalistic gene regulatory network model for the differentiation of macrophages into the two phenotypes M1 (pro-) and M2 (anti-inflammatory).

The angle of directional change of tracer trajectories in rotating Rayleigh-Benard convection is studied as a function of the time increment tau between two instants of time along the trajectories, both experimentally and with direct numerical simulations. Our aim is to explore the geometrical characterization of flow structures in turbulent convection in a wide range of timescales and how it is affected by background rotation.

Particle-laden turbulent flows occur in a variety of industrial applications as well as in naturally occurring flows. While the numerical simulation of such flows has seen significant advances in recent years, it still remains a challenging problem. Many studies investigated the rheology of dense suspensions in laminar flows as well as the dynamics of point-particles in turbulence.

Particle laden turbulent flows occur in a variety of industrial applications. While the numerical simulation of such flows has seen significant advances in recent years, it still remains a challenging problem. Many studies investigated the rheology of dense suspensions in laminar flows as well as the dynamics of point-particles in turbulence. Here we will present results on the development of numerical algorithms, based on the lattice Boltzmann method, suitable for the study of suspensions of finite-size particles under turbulent flow conditions.

We use high-resolution direct numerical simulations to study the anisotropic contents of a turbulent, statistically homogeneous flow with random transitions among multiple energy containing states. We decompose the velocity correlation functions on different sectors of the three-dimensional group of rotations, SO(3), using a high-precision quadrature. Scaling properties of anisotropic components of longitudinal and transverse velocity fluctuations are accurately measured at changing Reynolds numbers.

The Stokes drag force and the gravity force are usually sufficient to describe the behavior of sub-Kolmogorovsize (or pointlike) heavy particles in turbulence, in particular when the particle-to-fluid density ratio rho(p)/rho(integral) greater than or similar to 10(3) (with rho(p) and rho(f) the particle and fluid density, respectively). This is, in general, not the case for smaller particle-to-fluid density ratios, in particular not for rho(p)/rho(f) greater than or similar to 10(2).