514 research outputs found
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
- …