Transport dynamics of ultracold atoms in a triple-well transistor-like potential

The transport of atoms is experimentally studied in a transistor-like triple-well potential consisting of a narrow gate well surrounded by source and drain wells. Atoms are initially loaded into the source well with pre-determined temperature and chemical potential. Energetic atoms flow from the source, across the gate, and into the drain where they are removed using a resonant light beam. The manifestation of atom-atom interactions and dissipation is evidenced by a rapid population growth in the initially vacant gate well. The transport dynamics are shown to depend strongly on a feedback parameter determined by the relative heights of the two barriers forming the gate region. For a range of feedback parameter values, experiments establish that the gate atoms develop a larger chemical potential and lower temperature than those in the source.Comment: 13 pages, 5 figures, accepted for publication in NJ

Collapse and revival of the monopole mode of a degenerate Bose gas in an isotropic harmonic trap

We study the monopole (breathing) mode of a finite temperature Bose-Einstein condensate in an isotropic harmonic trap recently developed by Lobser et al. [Nat. Phys. 11, 1009 (2015)]. We observe a nonexponential collapse of the amplitude of the condensate oscillation followed by a partial revival. This behavior is identified as being due to beating between two eigenmodes of the system, corresponding to in-phase and out-of-phase oscillations of the condensed and noncondensed fractions of the gas. We perform finite temperature simulations of the system dynamics using the Zaremba-Nikuni-Griffin methodology [J. Low Temp. Phys. 116, 277 (1999)], and find good agreement with the data, thus confirming the two mode description

The Entropy Production Fluctuation Theorem and the Nonequilibrium Work Relation for Free Energy Differences

There are only a very few known relations in statistical dynamics that are valid for systems driven arbitrarily far-from-equilibrium. One of these is the fluctuation theorem, which places conditions on the entropy production probability distribution of nonequilibrium systems. Another recently discovered far-from-equilibrium expression relates nonequilibrium measurements of the work done on a system to equilibrium free energy differences. In this paper, we derive a generalized version of the fluctuation theorem for stochastic, microscopically reversible dynamics. Invoking this generalized theorem provides a succinct proof of the nonequilibrium work relation.Comment: 6 pages, 5 figures. Typos removed, references added. Includes an expanded introductio

PCR-GLOBWB 2: a 5 arcmin global hydrological and water resources model

We present PCR-GLOBWB 2, a global hydrology and water resources model. Compared to previous versions of PCR-GLOBWB, this version fully integrates water use. Sector-specific water demand, groundwater and surface water withdrawal, water consumption, and return flows are dynamically calculated at every time step and interact directly with the simulated hydrology. PCR-GLOBWB 2 has been fully rewritten in Python and PCRaster Python and has a modular structure, allowing easier replacement, maintenance, and development of model components. PCR-GLOBWB 2 has been implemented at 5 arcmin resolution, but a version parameterized at 30 arcmin resolution is also available. Both versions are available as open-source codes on https://github.com/UU-Hydro/PCR-GLOBWB_model (Sutanudjaja et al., 2017a). PCR-GLOBWB 2 has its own routines for groundwater dynamics and surface water routing. These relatively simple routines can alternatively be replaced by dynamically coupling PCR-GLOBWB 2 to a global two-layer groundwater model and 1-D–2-D hydrodynamic models. Here, we describe the main components of the model, compare results of the 30 and 5 arcmin versions, and evaluate their model performance using Global Runoff Data Centre discharge data. Results show that model performance of the 5 arcmin version is notably better than that of the 30 arcmin version. Furthermore, we compare simulated time series of total water storage (TWS) of the 5 arcmin model with those observed with GRACE, showing similar negative trends in areas of prevalent groundwater depletion. Also, we find that simulated total water withdrawal matches reasonably well with reported water withdrawal from AQUASTAT, while water withdrawal by source and sector provide mixed results

Effect of the integration method on the accuracy and computational efficiency of free energy calculations using thermodynamic integration

Although calculations of free energy using molecular dynamics simulations have gained significant importance in the chemical and biochemical fields, they still remain quite computationally intensive. Furthermore, when using thermodynamic integration, numerical evaluation of the integral of the Hamiltonian with respect to the coupling parameter may introduce unwanted errors in the free energy. In this paper, we compare the performance of two numerical integration techniques-the trapezoidal and Simpson's rules and propose a new method, based on the analytic integration of physically based fitting functions that are able to accurately describe the behavior of the data. We develop and test our methodology by performing detailed studies on two prototype systems, hydrated methane and hydrated methanol, and treat Lennard-Jones and electrostatic contributions separately. We conclude that the widely used trapezoidal rule may introduce systematic errors in the calculation, but these errors are reduced if Simpson's rule is employed, at least for the electrostatic component. Furthermore, by fitting thermodynamic integration data, we are able to obtain precise free energy estimates using significantly fewer data points (5 intermediate states for the electrostatic component and 11 for the Lennard-Jones term), thus significantly decreasing the associated computational cost. Our method and improved protocol were successfully validated by computing the free energy of more complex systems hydration of 2-methylbutanol and of 4-nitrophenol-thus paving the way for widespread use in solvation free energy calculations of drug molecules

Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strength of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide