Multistate Extension Research Articles

Fragment quantum embedding using the Householder transformation: A multi-state extension based on ensembles

In recent studies by Yalouz et al. [J. Chem. Phys. 157, 214112 (2022)] and Sekaran et al. [Phys. Rev. B 104, 035121 (2021) and Computation 10, 45 (2022)], density matrix embedding theory (DMET) has been reformulated through the use of the Householder transformation as a novel tool to embed a fragment within extended systems. The transformation was applied to a reference non-interacting one-electron reduced density matrix to construct fragments’ bath orbitals, which are crucial for subsequent ground state calculations. In the present work, we expand upon these previous developments and extend the utilization of the Householder transformation to the description of multiple electronic states, including ground and excited states. Based on an ensemble noninteracting density matrix, we demonstrate the feasibility of achieving exact fragment embedding through successive Householder transformations, resulting in a larger set of bath orbitals. We analytically prove that the number of additional bath orbitals scales directly with the number of fractionally occupied natural orbitals in the reference ensemble density matrix. A connection with the regular DMET bath construction is also made. Then, we illustrate the use of this ensemble embedding tool in single-shot DMET calculations to describe both ground and first excited states in a Hubbard lattice model and an ab initio hydrogen system. Finally, we discuss avenues for enhancing ensemble embedding through self-consistency and explore potential future directions.

Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory.

Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear-electronic coupling in addition to accurately predicting Franck-Condon vertical excitations. In this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, s-trans-butadiene, phenol, and cytosine.

Linearized Pair-Density Functional Theory for Vertical Excitation Energies.

Multiconfiguration pair-density functional theory (MC-PDFT) is a computationally efficient method that computes the energies of electronic states in a state specific or state average framework via an on-top functional. However, MC-PDFT does not include state interaction among these states since the final energies do not come from the diagonalization of an effective model-space Hamiltonian. Recently, multistate extensions such as linearized PDFT (L-PDFT) have been developed to accurately model the potentials near conical intersections and avoided crossings. However, there has not been any systematic study evaluating their performance for predicting vertical excitations at the equilibrium geometry of a molecule, when the excited states are generally well separated. In this paper, we report the performance of L-PDFT on the extensive QUESTDB data set of vertical excitations using a database of automatically selected active spaces. We show that L-PDFT performs well on all these excitations and successfully reproduces the performance of MC-PDFT. These results further demonstrate the potential of L-PDFT, as its scaling is constant with the number of states included in the state-average manifold, whereas MC-PDFT scales linearly in this regard.

Multi-state extension publication series highlights benefits of consumer horticulture to society and provides basis for further education efforts

ISHS XV International People Plant Symposium and II International Symposium on Horticultural Therapies: the Role of Horticulture in Human Well-being and Social Development Multi-state extension publication series highlights benefits of consumer horticulture to society and provides basis for further education efforts

New theoretical methods for the exploration of functional landscapes

AbstractMolecular functionality can be often directly attributed to given properties of the electronic wavefunction. Analogous to the potential energy surface, these properties can be represented as a function of the nuclear coordinates, giving rise to molecular “functional landscapes.” However, so far there has been no possibility for their systematic investigation. This perspective aims to discuss the development of new theoretical methods based on the multistate extension of the metadynamics approach, employing electronic collective variables. This emerging methodology allows to explore functional landscapes and to gain a deeper understanding of the structure–function relation in molecules and complex molecular systems in the ground and excited electronic state.

Nonhomogeneous Markov chain for estimating the cumulative risk of multiple false positive screening tests.

Screening tests are widely recommended for the early detection of disease among asymptomatic individuals. While detecting disease at an earlier stage has the potential to improve outcomes, screening also has negative consequences, including false positive results which may lead to anxiety, unnecessary diagnostic procedures, and increased healthcare costs. In addition, multiple false positive results could discourage participating in subsequent screening rounds. Screening guidelines typically recommend repeated screening over a period of many years, but little prior research has investigated how often individuals receive multiple false positive test results. Estimating the cumulative risk of multiple false positive results over the course of multiple rounds of screening is challenging due to the presence of censoring and competing risks, which may depend on the false positive risk, screening round, and number of prior false positive results. To address the general challenge of estimating the cumulative risk of multiple false positive test results, we propose a nonhomogeneous multistate model to describe the screening process including competing events. We developed alternative approaches for estimating the cumulative risk of multiple false positive results using this multistate model based on existing estimators for the cumulative risk of a single false positive. We compared the performance of the newly proposed models through simulation studies and illustrate model performance using data on screening mammography from the Breast Cancer Surveillance Consortium. Across most simulation scenarios, the multistate extension of a censoring bias model demonstrated lower bias compared to other approaches. In the context of screening mammography, we found that the cumulative risk of multiple false positive results is high. For instance, based on the censoring bias model, for a high-risk individual, the cumulative probability of at least two false positive mammography results after 10 rounds of annual screening is 40.4.

Many-electron effects of strong-field ionization described in an exact one-electron theory

If one-electron observables of a many-electron system are of interest, a many-electron dynamics can be represented exactly by a one-electron dynamics with effective potentials. The formalism for this reduction is provided by the Exact Electron Factorization (EEF). We study the time-dependent features of the EEF effective potentials for a model of an atom ionized by an ultrastrong and ultrashort laser pulse, with the aim of understanding what is needed to develop computationally feasible approximations. It is found that the simplest approximation, the so-called time-independent conditional amplitude (TICA) approximation, is complementary to single-active electron (SAE) approaches as it reproduced the exact dynamics well for high photon frequencies of the laser field or large Keldysh parameter. For relatively low frequencies of the laser field or for smaller Keldysh parameters, we find that excited state dynamics in the core region of the atom leads to a time-dependent ionization barrier in the EEF potential. The time-dependence of the barrier needs to be described accurately to correctly model many-electron effects, and we conclude that a multi-state extension of the TICA approximation is a possible route how this can be achieved. In general, our study sheds a different light on one-electron pictures of strong-field ionization and shows that many-electron effects for such processes may be included by solving a one-electron Schr\"odinger equation, provided the core dynamics can be modeled successfully.

Evaluation of Farm Fresh Food Boxes: A Hybrid Alternative Food Network Market Innovation

Using a mixed-methods design, we evaluated Farm Fresh Food Box (F3B) a market innovation designed to expand producer markets, stabilize rural retail businesses, and improve rural food access. In the F3B model, pre-ordered Community Supported Agriculture (CSA)-style produce boxes are sold through rural retail outlets. F3B was implemented from 2016 to 2018 as part of a United States Department of Agriculture (USDA)-funded multi-state extension and research collaboration project in 3 geographically diverse and rural areas: Vermont, Washington, and California. The F3B evaluation aimed to (1) assess market potential; (2) determine logistics for successful implementation; (3) describe the benefits and drawbacks for farmers and retailers; and (4) measure consumers’ attitudes and purchase behavior. A national market survey indicated consumers would be likely to purchase F3B if it was perceived to offer good value on fresh local produce, without need for a subscription. The model put a few additional labor burdens on farmers and retailers, but required time for relationship-building and more record-keeping time for farmers. Those who purchased a F3B were generally satisfied with the quality, quantity and variety of produce each week and a high proportion considered F3B to be a good value for the money. As a new business innovation, F3B showed only modest profit, but retailers and farmers felt it was worthwhile to expand their customer base, promote their brand and develop their partnership. F3B began a means to address flattened growth in direct to consumer produce sales, food deserts and dwindling retail options for fresh foods in rural areas. We discuss F3B as a potential solution to food system weaknesses exposed by the COIVD-19 pandemic because it offers touch-free, high-quality local produce ready for curbside pickup at a convenient location.

A Brief Report on a Facilitated Approach to Connect Cooperative Extension Southern Region State-Level Health Specialists

Improving the nation’s health will require collaboration among many stakeholders and systems, including representatives from Cooperative Extension Services (CES). This paper describes the process of establishing a multistate collaboration and discusses initial outcomes of a third-party facilitated participatory planning meeting. State-level specialists with expertise and responsibilities in “health” promotion participated. Satisfaction with meeting format; feasibility, acceptability, and appropriateness of the proposed approach to public health impact; and general meeting feedback were collected through a survey and cultural artifacts (e.g., notes, worksheets). Preparation and attendance costs were captured. Seventeen of the 20 attendees (85%) responded to the survey and reported the process was satisfactory and the proposed plan for moving forward was feasible, acceptable, and appropriate. The meeting cost was $1,011 per attendee. The process mobilized a multistate Extension collaborative to promote health but revealed potential cost-benefit challenges. Leveraging resources is necessary to plan, implement, and measure collaborative public health efforts. Future data on outcomes will show if the process leads to intended objectives. If successful, this approach can be replicated across CES for stronger impacts.

Bias-Corrected Q-Learning With Multistate Extension

Q-learning is a sample-based model-free algorithm that solves Markov decision problems asymptotically, but in finite time, it can perform poorly when random rewards and transitions result in large variance of value estimates. We pinpoint its cause to be the estimation bias due to the maximum operator in Q-learning algorithm, and present the evidence of max-operator bias in its Q value estimates. We then present an asymptotically optimal bias-correction strategy and construct an extension to bias-corrected Q-learning algorithm to multistate Markov decision processes, with asymptotic convergence properties as strong as those from Q-learning. We report the empirical performance of the bias-corrected Q-learning algorithm with multistate extension in two model problems: A multiarmed bandit version of Roulette and an electricity storage control simulation. The bias-corrected Q-learning algorithm with multistate extension is shown to control max-operator bias effectively, where the bias-resistance can be tuned predictably by adjusting a correction parameter.

OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.

Transition path sampling techniques allow molecular dynamics simulations of complex systems to focus on rare dynamical events, providing insight into mechanisms and the ability to calculate rates inaccessible by ordinary dynamics simulations. While path sampling algorithms are conceptually as simple as importance sampling Monte Carlo, the technical complexity of their implementation has kept these techniques out of reach of the broad community. Here, we introduce an easy-to-use Python framework called OpenPathSampling (OPS) that facilitates path sampling for (bio)molecular systems with minimal effort and yet is still extensible. Interfaces to OpenMM and an internal dynamics engine for simple models are provided in the initial release, but new molecular simulation packages can easily be added. Multiple ready-to-use transition path sampling methodologies are implemented, including standard transition path sampling (TPS) between reactant and product states and transition interface sampling (TIS) and its replica exchange variant (RETIS), as well as recent multistate and multiset extensions of transition interface sampling (MSTIS, MISTIS). In addition, tools are provided to facilitate the implementation of new path sampling schemes built on basic path sampling components. In this paper, we give an overview of the design of this framework and illustrate the simplicity of applying the available path sampling algorithms to a variety of benchmark problems.

15 A Stockmanship and Stewardship Regional Event Combined with the Deep South Stocker Conference: Multi-State Extension Programming for Beef Producers.

15 A Stockmanship and Stewardship Regional Event Combined with the Deep South Stocker Conference: Multi-State Extension Programming for Beef Producers.

Advancing Integrated Pest Management Adoption and Achieving Extension Impact: A Working Group Success Story

Extension and research professionals in the southeastern United States formed the Southern Nursery Integrated Pest Management working group (SNIPM) to foster collaboration and leverage resources, thereby enhancing extension programming, increasing opportunity, and expanding the delivery of specialized expertise to nursery crop growers across a region. Building a productive and lasting working group requires attracting a group of research and extension faculty with complementary expertise, listening to stakeholders, and translating stakeholder needs into grant priorities to help solve problems, all hallmarks of effective teamwork principles. SNIPM has now grown to include 10 U.S. states and 11 institutions and has been awarded seven grants totaling $190,994 since 2009. A striking benefit of working group membership was observed over time: synergy. Greater awareness of individual expertise among SNIPM members, each of whom were focused on different aspects of the nursery production system stimulated multistate extension publications, electronic books (eBooks), mobile device applications (apps), popular press articles, and spin-off research projects when separate foci were combined and directed toward complex challenges. Deliverables achieved from this faculty collaboration include nine peer-reviewed publications, four manuals and books and 23 book chapters, and a combined total of 11 abstracts, conference proceedings and extension publications. To date, the return on investment for SNIPM is one deliverable produced to every $2265.89 in grant funding. SNIPM has also been honored with multiple American Society for Horticultural Science publication awards as well as the Southern Region Integrated Pest Management Center Bright Idea Award for the quality and originality of their project outputs. Continuing to work together toward common goals that bridge technology and serve the nursery industry while supporting each individual member’s program will be crucial to the long-term success of this working group.

Promoting Access to Health Insurance through a Multistate Extension Collaboration

This paper describes a multistate project that addressed the growing need for health insurance information for individuals by focusing on the Affordable Care Act (ACA) and health insurance education and outreach efforts in targeted areas of the country in federally-facilitated marketplaces with high numbers of uninsured and underinsured individuals. Specifically, the project provided ACA and health insurance information to individuals in formal and informal settings to assist them in choosing a health insurance plan through the Marketplace. Education and outreach activities included group workshops and presentations, Q&A sessions, and panel discussions; one-on-one in-person consultations, phone consultations, and email consultations; and information provided through websites, blog posts, Facebook posts, tweets, YouTube videos, email blasts, newsletters, newspaper articles, and radio and TV programs. Health insurance enrollment assistance was provided by volunteers and some Extension educators or referrals were made to Navigators or Certified Application Counselors for enrollment assistance.

0594 Developing regional and multi-state extension collaborations

0594 Developing regional and multi-state extension collaborations

Driving initiatives for future improvements of specialty agricultural crops

Today the global world is faced to address and meet the key challenges of agricultural development reliant on research and innovation actions. One of these actions is especially linked to the socio-economic requirements, foundational resources and rights of farmers to support agricultural production and outputs. As an agricultural output, some agricultural crops are proposed to satisfy as specialty agricultural crops according to the local and regional needs to enable improvements for all parties to provide good income, promotes equity, growth better livelihood and agricultural employment. These crops have some specific features and become increasingly important to have influenced on regional, national and multi-state agricultural research, development and extension initiatives. And also, they have leading effects on (i) food security, (ii) livelihood security and (iii) agricultural and rural development to make integration with the criteria such as economically significance, interests and feasibility of parties. Although the Agriculture Modality Paper, for agricultural issues released by The Chairman of the World Trade Organization (WTO) Negotiations on Agriculture, covers some criteria helping to define these crops, exactly there have been no globally common standards for identification them. However, it is questioned that how develop the specialty agricultural crops beyond identification of them. In this paper, firstly, it is aimed to address the key needs for future improvements of specialty agricultural crops. This mainly for designation of a framework for these crops covering all components in respond to this question integrated with agricultural innovation units and agricultural development sustainability within the innovation including their attributes and dimensions. Further, this schema focused on the prerequisites framework within the key priorities and the initiatives of innovation based specialty agricultural growth to make integration with ongoing agricultural policy and practice around the world. In follows, it is described the innovation units to improve production efficiency for specialty agricultural crops. Finally, it is represented the attributes and dimensions of sustainability with innovation through the specialty agricultural crop development. Integrated all these stages would provide a basis and methodology for sustainable specialty agricultural crops development strategies, growing under state guarantee in several world countries, following the drivers of agricultural innovation. And also it is expected to contribute to create an opportunity for farmers/organizations to produce such crops by accelerating the rate of innovation adoption within well-established priorities in agricultural rights. So, it is enabled to have an ability to cope with the effects of global agricultural challenges and emerging opportunities.

Multi-state Asymmetric Simple Exclusion Processes

It is known that the Markov matrix of the asymmetric simple exclusion process (ASEP) is invariant under the Uq(sl2) algebra. This is the result of the fact that the Markov matrix of the ASEP coincides with the generator of the Temperley-Lieb (TL) algebra, the dual algebra of the Uq(sl2) algebra. Various types of algebraic extensions have been considered for the ASEP. In this paper, we considered the multi-state extension of the ASEP, by allowing more than two particles to occupy the same box. We constructed the Markov matrix by dimensionally extending the TL generators and derived explicit forms of the particle densities and the currents on the steady states. Then we showed how decay lengths differ from the original two-state ASEP under the closed boundary conditions.

Diversitree: comparative phylogenetic analyses of diversification in R

Summary1. The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary state speciation and extinction), MuSSE (a multistate extension of BiSSE), and QuaSSE (quantitative state speciation and extinction). Diversitree also includes methods for analysing trait evolution and estimating speciation/extinction rates independently.2. In this note, I describe the features and demonstrate use of the package, using a new method, MuSSE (multistate speciation and extinction), to examine the joint effects of two traits on speciation.3. Using simulations, I found that MuSSE could reliably detect that a binary trait that affected speciation rates when simultaneously accounting for additional thats that had no effect on speciation rates.4. Diversitree is an open source and available on the Comprehensive R Archive Network (cran). A tutorial and worked examples can be downloaded from http://www.zoology.ubc.ca/prog/diversitree.

Getting Mixed-Up: Are Greenhouse Producers Adopting Appropriate Pesticide Mixtures to Manage Arthropod Pests?

Pesticide mixtures are commonly used by greenhouse producers to deal with the array of arthropod (insect and mite) pests encountered in greenhouses. Greenhouse producers tank mix pesticides due to convenience because it is less time consuming, costly, and labor intensive to mix together two or more pesticides into a single spray solution and then perform one spray application compared with making multiple applications. Pesticide mixtures may also result in improved arthropod pest control. However, there has been no quantitative assessment to determine what pesticide mixtures (two-, three-, and four-way combinations) are being adopted by greenhouse producers and why. As such, a survey was conducted by distributing evaluation forms in conjunction with three sessions at two greenhouse producer conferences (two in 2007 and one in 2008) to obtain data on the types of pesticide mixtures used by greenhouse producers and determine if there are any problems associated with these pesticide mixtures. The evaluation form requested that participants provide information on the four most common pesticide mixtures (insecticides and/or miticides) used and for what specific arthropod pests. The response rate of the evaluation forms was 22.5% (45/200). The two-way pesticide mixture that was cited most often (n = 8) was the abamectin (Avid) and bifenthrin (Talstar) combination. The two pesticides typically included in a majority of the two-way and three-way mixtures were spinosad (Conserve) and abamectin. Spinosad was a component of 17 two-way and 7 three-way combinations, while abamectin was cited in 15 two-way and 9 three-way combinations. Both products are labeled for control of the western flower thrips (Frankliniella occidentalis), which is one of the most important insect pests in greenhouses. One pesticide mixture that was difficult to interpret involved the fungicides, thiophanate-methyl (Cleary's 3336) and metalaxyl (Subdue). This mixture was cited twice, and the arthropod pest listed was thrips (Thysanoptera). However, both fungicides have no insecticidal activity. Two of the mixtures listed in the survey used pesticides with similar modes of action: acephate (Orthene) + methiocarb (Mesurol), and pyrethrins (Pyreth-It) + bifenthrin (Talstar). A number of the pesticide mixtures listed for spider mites (Tetranychidae) were questionable due to similar life stage activity of the a.i. as indicated on the label including fenpyroximate (Akari) + clofentezine (Ovation), abamectin + chlorfenapyr (Pylon), and bifenazate (Floramite) + etoxazole (TetraSan). In fact, 38% of pesticide mixtures cited for twospotted spider mite (Tetranychus urticae) control should have been avoided due to analogous life stage activity. The data obtained from the survey clearly demonstrates that greenhouse producers implement a wide-range of pesticide mixtures to deal with the multitude of arthropod pests in greenhouses. However, the basis by which greenhouse producers decide the types of pesticides to mix together is not known. As such, the survey data can be used to direct future multistate or multiregional extension (outreach) efforts in developing programs specifically designed to educate greenhouse producers on which pesticides should and should not be mixed together.

Getting Mixed-Up: Are Greenhouse Producers Adopting Appropriate Pesticide Mixtures to Manage Arthropod Pests?

Pesticide mixtures are commonly used by greenhouse producers to deal with the array of arthropod (insect and mite) pests encountered in greenhouses. Greenhouse producers tank mix pesticides due to convenience because it is less time consuming, costly, and labor intensive to mix together two or more pesticides into a single spray solution and then perform one spray application compared with making multiple applications. Pesticide mixtures may also result in improved arthropod pest control. However, there has been no quantitative assessment to determine what pesticide mixtures (two-, three-, and four-way combinations) are being adopted by greenhouse producers and why. As such, a survey was conducted by distributing evaluation forms in conjunction with three sessions at two greenhouse producer conferences (two in 2007 and one in 2008) to obtain data on the types of pesticide mixtures used by greenhouse producers and determine if there are any problems associated with these pesticide mixtures. The evaluation form requested that participants provide information on the four most common pesticide mixtures (insecticides and/or miticides) used and for what specific arthropod pests. The response rate of the evaluation forms was 22.5% (45/200). The two-way pesticide mixture that was cited most often (n = 8) was the abamectin (Avid) and bifenthrin (Talstar) combination. The two pesticides typically included in a majority of the two-way and three-way mixtures were spinosad (Conserve) and abamectin. Spinosad was a component of 17 two-way and 7 three-way combinations, while abamectin was cited in 15 two-way and 9 three-way combinations. Both products are labeled for control of the western flower thrips (Frankliniella occidentalis), which is one of the most important insect pests in greenhouses. One pesticide mixture that was difficult to interpret involved the fungicides, thiophanate-methyl (Cleary's 3336) and metalaxyl (Subdue). This mixture was cited twice, and the arthropod pest listed was thrips (Thysanoptera). However, both fungicides have no insecticidal activity. Two of the mixtures listed in the survey used pesticides with similar modes of action: acephate (Orthene) + methiocarb (Mesurol), and pyrethrins (Pyreth-It) + bifenthrin (Talstar). A number of the pesticide mixtures listed for spider mites (Tetranychidae) were questionable due to similar life stage activity of the a.i. as indicated on the label including fenpyroximate (Akari) + clofentezine (Ovation), abamectin + chlorfenapyr (Pylon), and bifenazate (Floramite) + etoxazole (TetraSan). In fact, 38% of pesticide mixtures cited for twospotted spider mite (Tetranychus urticae) control should have been avoided due to analogous life stage activity. The data obtained from the survey clearly demonstrates that greenhouse producers implement a wide-range of pesticide mixtures to deal with the multitude of arthropod pests in greenhouses. However, the basis by which greenhouse producers decide the types of pesticides to mix together is not known. As such, the survey data can be used to direct future multistate or multiregional extension (outreach) efforts in developing programs specifically designed to educate greenhouse producers on which pesticides should and should not be mixed together.