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

Nonlinear viscoelasticity of metastable complex fluids

Many metastable complex fluids such as colloidal glasses and gels show distinct nonlinear viscoelasticity with increasing oscillatory-strain amplitude; the storage modulus decreases monotonically as the strain amplitude increases whereas the loss modulus has a distinct peak before it decreases at larger strains. We present a qualitative argument to explain this ubiquitous behavior and use mode coupling theory (MCT) to confirm it. We compare theoretical predictions to the measured nonlinear viscoelasticity in a dense hard sphere colloidal suspensions; reasonable agreement is obtained. The argument given here can be used to obtain new information about linear viscoelasticity of metastable complex fluids from nonlinear strain measurements.Comment: 7 pages, 3 figures, accepted for publication in Europhys. Let

Expert-Augmented Machine Learning

Machine Learning is proving invaluable across disciplines. However, its success is often limited by the quality and quantity of available data, while its adoption by the level of trust that models afford users. Human vs. machine performance is commonly compared empirically to decide whether a certain task should be performed by a computer or an expert. In reality, the optimal learning strategy may involve combining the complementary strengths of man and machine. Here we present Expert-Augmented Machine Learning (EAML), an automated method that guides the extraction of expert knowledge and its integration into machine-learned models. We use a large dataset of intensive care patient data to predict mortality and show that we can extract expert knowledge using an online platform, help reveal hidden confounders, improve generalizability on a different population and learn using less data. EAML presents a novel framework for high performance and dependable machine learning in critical applications

Time reparametrization invariance in arbitrary range p-spin models: symmetric versus non-symmetric dynamics

We explore the existence of time reparametrization symmetry in p-spin models. Using the Martin-Siggia-Rose generating functional, we analytically probe the long-time dynamics. We perform a renormalization group analysis where we systematically integrate over short timescale fluctuations. We find three families of stable fixed points and study the symmetry of those fixed points with respect to time reparametrizations. One of those families is composed entirely of symmetric fixed points, which are associated with the low temperature dynamics. The other two families are composed entirely of non-symmetric fixed points. One of these two non-symmetric families corresponds to the high temperature dynamics. Time reparametrization symmetry is a continuous symmetry that is spontaneously broken in the glass state and we argue that this gives rise to the presence of Goldstone modes. We expect the Goldstone modes to determine the properties of fluctuations in the glass state, in particular predicting the presence of dynamical heterogeneity.Comment: v2: Extensively modified to discuss both high temperature (non-symmetric) and low temperature (symmetric) renormalization group fixed points. Now 16 pages with 1 figure. v1: 13 page

Cumulant Expansions and the Spin-Boson Problem

The dynamics of the dissipative two-level system at zero temperature is studied using three different cumulant expansion techniques. The relative merits and drawbacks of each technique are discussed. It is found that a new technique, the non-crossing cumulant expansion, appears to embody the virtues of the more standard cumulant methods.Comment: 26 pages, LaTe

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

Glasslike Arrest in Spinodal Decomposition as a Route to Colloidal Gelation

Colloid-polymer mixtures can undergo spinodal decomposition into colloid-rich and colloid-poor regions. Gelation results when interconnected colloid-rich regions solidify. We show that this occurs when these regions undergo a glass transition, leading to dynamic arrest of the spinodal decomposition. The characteristic length scale of the gel decreases with increasing quench depth, and the nonergodicity parameter exhibits a pronounced dependence on scattering vector. Mode coupling theory gives a good description of the dynamics, provided we use the full static structure as input.Comment: 14 pages, 4 figures; replaced with published versio

Pollen-Mediated Gene Flow from Genetically Modified Herbicide Resistant Creeping Bentgrass

Approximately 162 ha of multiple experimental fields of creeping bentgrass (Agrostis stolonifera L.) genetically modified for resistance to Roundup ®herbicide, were planted in central Oregon in 2002. When the fields flowered for the first time in the summer of 2003, a unique opportunity was presented to evaluate methods to monitor potential pollen-mediated gene flow from the experimental GM crop fields to compatible sentinel and resident plants that were located in surrounding, primarily non-agronomic areas

Growing dynamical length, scaling and heterogeneities in the 3d Edwards-Anderson model

We study numerically spatio-temporal fluctuations during the out-of-equilibrium relaxation of the three-dimensional Edwards-Anderson model. We focus on two issues. (1) The evolution of a growing dynamical length scale in the glassy phase of the model, and the consequent collapse of the distribution of local coarse-grained correlations measured at different pairs of times on a single function using {\it two} scaling parameters, the value of the global correlation at the measuring times and the ratio of the coarse graining length to the dynamical length scale (in the thermodynamic limit). (2) The `triangular' relation between coarse-grained local correlations at three pairs of times taken from the ordered instants $t_3 \leq t_2 \leq t_1$. Property (1) is consistent with the conjecture that the development of time-reparametrization invariance asymptotically is responsible for the main dynamic fluctuations in aging glassy systems as well as with other mechanisms proposed in the literature. Property (2), we stress, is a much stronger test of the relevance of the time-reparametrization invariance scenario.Comment: 24 pages, 12 fig

Quantum fluctuations can promote or inhibit glass formation

The very nature of glass is somewhat mysterious: while relaxation times in glasses are of sufficient magnitude that large-scale motion on the atomic level is essentially as slow as it is in the crystalline state, the structure of glass appears barely different than that of the liquid that produced it. Quantum mechanical systems ranging from electron liquids to superfluid helium appear to form glasses, but as yet no unifying framework exists connecting classical and quantum regimes of vitrification. Here we develop new insights from theory and simulation into the quantum glass transition that surprisingly reveal distinct regions where quantum fluctuations can either promote or inhibit glass formation.Comment: Accepted for publication in Nature Physics. 22 pages, 3 figures, 1 Tabl