IBIS2.0: The new Interferometric BIdimensional Spectrometer

We present the IBIS2.0 project, which aims to upgrade and to install the Interferometric BIdimensional Spectrometer at the solar Vacuum Tower Telescope (Tenerife, Spain) after its disassembling from the Dunn Solar Telescope (New Mexico, USA). The instrument is undergoing a hardware and software revision that will allow it to perform new spectropolarimetric measurements of the solar atmosphere at high spatial, spectral and temporal resolution in coordination with other ground- and space-based instruments. Here we present the new opto-mechanical layout and control system designed for the instrument, and describe future steps...

Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude

An important issue concerning computer simulations addressed to free energy estimates via nonequilibrium work theorems, such as the Jarzynski equality [Phys. Rev. Lett. 1997, 78, 2690], is the computational effort required to achieve results with acceptable accuracy. In this respect, the dynamical freezing approach [Phys. Rev. E 2009, 80, 041124] has been shown to improve the efficiency of this kind of simulations, by blocking the dynamics of particles located outside an established mobility region. In this report, we show that dynamical freezing produces a systematic spurious decrease of the particle density inside the mobility region. As a consequence, the requirements to apply nonequilibrium work theorems are only approximately met. Starting from these considerations, we have developed a simulation scheme, called “elastic barrier dynamical freezing”, according to which a stiff potential-energy barrier is enforced at the boundaries of the mobility region, preventing the particles from leaving this region of space during the nonequilibrium trajectories. The method, tested on the calculation of the distance-dependent free energy of a dimer immersed into a Lennard-Jones fluid, provides an accuracy comparable to the conventional steered molecular dynamics, with a computational speedup exceeding a few orders of magnitude

Nonequilibrium Candidate Monte Carlo Simulations with Configurational Freezing Schemes

Nonequilibrium Candidate Monte Carlo simulation [Nilmeier et al., <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>2011</b>, <i>108</i>, E1009–E1018] is a tool devised to design Monte Carlo moves with high acceptance probabilities that connect uncorrelated configurations. Such moves are generated through nonequilibrium driven dynamics, producing candidate configurations accepted with a Monte Carlo-like criterion that preserves the equilibrium distribution. The probability of accepting a candidate configuration as the next sample in the Markov chain basically depends on the work performed on the system during the nonequilibrium trajectory and increases with decreasing such a work. It is thus strategically relevant to find ways of producing nonequilibrium moves with low work, namely moves where dissipation is as low as possible. This is the goal of our methodology, in which we combine Nonequilibrium Candidate Monte Carlo with Configurational Freezing schemes developed by Nicolini et al. (<i>J. Chem. Theory Comput.</i> <b>2011</b>, <i>7</i>, 582–593). The idea is to limit the configurational sampling to particles of a well-established region of the simulation sample, namely the region where dissipation occurs, while leaving fixed the other particles. This allows to make the system relaxation faster around the region perturbed by the finite-time switching move and hence to reduce the dissipated work, eventually enhancing the probability of accepting the generated move. Our combined approach enhances significantly configurational sampling, as shown by the case of a bistable dimer immersed in a dense fluid

Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework

The fast-switching decoupling method is a powerful nonequilibrium technique to compute absolute binding free energies of ligand–receptor complexes (Sandberg et al., <i>J. Chem. Theory Comput</i>. <b>2014</b>, <i>11</i>, 423–435). Inspired by the theory of noncovalent binding association of Gilson and co-workers (<i>Biophys. J</i>. <b>1997</b>, <i>72</i>, 1047–1069), we develop two approaches, termed binded-domain and single-point alchemical-path schemes (BiD-AP and SiP-AP), based on the possibility of performing alchemical trajectories during which the ligand is constrained to fixed positions relative to the receptor. The BiD-AP scheme exploits a recent generalization of nonequilibrium work theorems to estimate the free energy difference between the coupled and uncoupled states of the ligand–receptor complex. With respect to the fast-switching decoupling method without constraints, BiD-AP prevents the ligand from leaving the binding site, but still requires an estimate of the positional binding-site volume, which may not be a simple task. On the other side, the SiP-AP scheme allows avoidance of the calculation of the binding-site volume by introducing an additional equilibrium simulation of ligand and receptor in the bound state. In the companion article (DOI: 10.1021/acs.jctc.7b00595), we show that the extra computational effort required by SiP-AP leads to a significant improvement of accuracy in the free energy estimates