Reduced density matrix hybrid approach: Application to electronic energy transfer

Electronic energy transfer in the condensed phase, such as that occurring in photosynthetic complexes, frequently occurs in regimes where the energy scales of the system and environment are similar. This situation provides a challenge to theoretical investigation since most approaches are accurate only when a certain energetic parameter is small compared to others in the problem. Here we show that in these difficult regimes, the Ehrenfest approach provides a good starting point for a dynamical description of the energy transfer process due to its ability to accurately treat coupling to slow environmental modes. To further improve on the accuracy of the Ehrenfest approach, we use our reduced density matrix hybrid framework to treat the faster environmental modes quantum mechanically, at the level of a perturbative master equation. This combined approach is shown to provide an efficient and quantitative description of electronic energy transfer in a model dimer and the Fenna-Matthews-Olson complex and is used to investigate the effect of environmental preparation on the resulting dynamics.Comment: 11 pages, 8 figure

Efficient stochastic thermostatting of path integral molecular dynamics

The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high-frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat which exploits an analytic knowledge of the free path integral normal mode frequencies. We also apply a recently-developed colored-noise thermostat based on a generalized Langevin equation (GLE), which automatically achieves a similar, frequency-optimized sampling. The sampling efficiencies of these thermostats are compared with that of the more conventional Nos\'e-Hoover chain (NHC) thermostat for a number of physically relevant properties of the liquid water and hydrogen-in-palladium systems. In nearly every case, the new PILE thermostat is found to perform just as well as the NHC thermostat while allowing for a computationally more efficient implementation. The GLE thermostat also proves to be very robust delivering a near-optimum sampling efficiency in all of the cases considered. We suspect that these simple stochastic thermostats will therefore find useful application in many future PIMD simulations.Comment: Accepted for publication on JC

Reduced density matrix hybrid approach: An efficient and accurate method for adiabatic and non-adiabatic quantum dynamics

We present a new approach to calculate real-time quantum dynamics in complex systems. The formalism is based on the partitioning of a system's environment into "core" and "reservoir" modes, with the former to be treated quantum mechanically and the latter classically. The presented method only requires the calculation of the system's reduced density matrix averaged over the quantum core degrees of freedom which is then coupled to a classically evolved reservoir to treat the remaining modes. We demonstrate our approach by applying it to the spin-boson problem using the noninteracting blip approximation to treat the system and core, and Ehrenfest dynamics to treat the reservoir. The resulting hybrid methodology is accurate for both fast and slow baths, since it naturally reduces to its composite methods in their respective regimes of validity. In addition, our combined method is shown to yield good results in intermediate regimes where neither approximation alone is accurate and to perform equally well for both strong and weak system-bath coupling. Our approach therefore provides an accurate and efficient methodology for calculating quantum dynamics in complex systems.Comment: 10 pages, 7 figure

Force transmission in a packing of pentagonal particles

We perform a detailed analysis of the contact force network in a dense confined packing of pentagonal particles simulated by means of the contact dynamics method. The effect of particle shape is evidenced by comparing the data from pentagon packing and from a packing with identical characteristics except for the circular shape of the particles. A counterintuitive finding of this work is that, under steady shearing, the pentagon packing develops a lower structural anisotropy than the disk packing. We show that this weakness is compensated by a higher force anisotropy, leading to enhanced shear strength of the pentagon packing. We revisit "strong" and "weak" force networks in the pentagon packing, but our simulation data provide also evidence for a large class of "very weak" forces carried mainly by vertex-to-edge contacts. The strong force chains are mostly composed of edge-to-edge contacts with a marked zig-zag aspect and a decreasing exponential probability distribution as in a disk packing

Urinary, Fecal, and Dual Incontinence in Older U.S. Adults

To estimate the prevalence of urinary (UI), fecal (FI), and dual incontinence (DI) and to identify shared factors associated with each type of incontinence in older U.S. women and men

A randomized controlled trial to evaluate self-determination theory for exercise adherence and weight control: rationale and intervention description

<p>Abstract</p> <p>Background</p> <p>Research on the motivational model proposed by Self-Determination Theory (SDT) provides theoretically sound insights into reasons why people adopt and maintain exercise and other health behaviors, and allows for a meaningful analysis of the motivational processes involved in behavioral self-regulation. Although obesity is notoriously difficult to reverse and its recidivism is high, adopting and maintaining a physically active lifestyle is arguably the most effective strategy to counteract it in the long-term. The purposes of this study are twofold: i) to describe a 3-year randomized controlled trial (RCT) aimed at testing a novel obesity treatment program based on SDT, and ii) to present the rationale behind SDT's utility in facilitating and explaining health behavior change, especially physical activity/exercise, during obesity treatment.</p> <p>Methods</p> <p>Study design, recruitment, inclusion criteria, measurements, and a detailed description of the intervention (general format, goals for the participants, intervention curriculum, and main SDT strategies) are presented. The intervention consists of a 1-year group behavioral program for overweight and moderately obese women, aged 25 to 50 (and pre-menopausal), recruited from the community at large through media advertisement. Participants in the intervention group meet weekly or bi-weekly with a multidisciplinary intervention team (30 2 h sessions in total), and go through a program covering most topics considered critical for successful weight control. These topics and especially their delivery were adapted to comply with SDT and Motivational Interviewing guidelines. Comparison group receive a general health education curriculum. After the program, all subjects are follow-up for a period of 2 years.</p> <p>Discussion</p> <p>Results from this RCT will contribute to a better understanding of how motivational characteristics, particularly those related to physical activity/exercise behavioral self-regulation, influence treatment success, while exploring the utility of Self-Determination Theory for promoting health behavior change in the context of obesity.</p> <p>Trial Registration</p> <p><b>Clinical Trials Gov. Identifier </b>NCT00513084</p

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated at the {\omega}B97M-D3(BJ)/def2-TZVPPD level of theory, along with other useful quantities such as multipole moments and bond orders. We train a set of machine learning potentials on it and demonstrate that they can achieve chemical accuracy across a broad region of chemical space. It can serve as a valuable resource for the creation of transferable, ready to use potential functions for use in molecular simulations.Comment: 19 pages, 6 figure

Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges

Nuclear quantum effects influence the structure and dynamics of hydrogen-bonded systems, such as water, which impacts their observed properties with widely varying magnitudes. This review highlights the recent significant developments in the experiment, theory, and simulation of nuclear quantum effects in water. Novel experimental techniques, such as deep inelastic neutron scattering, now provide a detailed view of the role of nuclear quantum effects in water's properties. These have been combined with theoretical developments such as the introduction of the principle of competing quantum effects that allows the subtle interplay of water's quantum effects and their manifestation in experimental observables to be explained. We discuss how this principle has recently been used to explain the apparent dichotomy in water's isotope effects, which can range from very large to almost nonexistent depending on the property and conditions. We then review the latest major developments in simulation algorithms and theory that have enabled the efficient inclusion of nuclear quantum effects in molecular simulations, permitting their combination with on-the-fly evaluation of the potential energy surface using electronic structure theory. Finally, we identify current challenges and future opportunities in this area of research

Effects of colpocleisis on bowel symptoms among women with severe pelvic organ prolapse

Our objective was to evaluate bowel symptoms after colpocleisis