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An assessment of the load modifying potential of model predictive controlled dynamic facades within the California context
California is making major strides towards meeting its greenhouse gas emission reduction goals with the transformation of its electrical grid to accommodate renewable generation, aggressive promotion of building energy efficiency, and increased emphasis on moving toward electrification of end uses (e.g., residential heating, etc.). As a result of this activity, the State is faced with significant challenges of systemwide resource adequacy, power quality and grid reliability that could be addressed in part with demand responsive (DR) load modifying strategies using controllable building technologies. Dynamic facades have the ability to potentially shift and shed loads at critical times of the day in combination with daylighting and HVAC controls. This study explores the technical potential of dynamic facades to support net load shape objectives. A model predictive controller (MPC) was designed based on reduced order thermal (Modelica) and window (Radiance) models. Using an automated workflow (involving JModelica.org and MPCPy), these models were converted and differentiated to formulate a non-linear optimization problem. A gradient-based, non-linear programming problem solver (IPOPT) was used to derive an optimal control strategy, then a post-optimization step was used to convert the solution to a discrete state for facade actuation. Continuous state modulation of the façade was also modeled. The performance of the MPC controller with and without activation of thermal mass was evaluated in a south-facing perimeter office zone with a three-zone electrochromic window for a clear sunny week during summer and winter periods in Oakland and Burbank, California. MPC strategies reduced total energy cost by 9–28% and critical coincident peak demand was reduced by up to 0.58 W/ft2-floor or 19–43% in the 4.6 m (15 ft) deep south zone on sunny summer days in Oakland compared to state-of-the-art heuristic control. Similar savings were achieved for the hotter, Burbank climate in Southern California. This outcome supports the argument that MPC control of dynamic facades can provide significant electricity cost reductions and net load management capabilities of benefit to both the building owner and evolving electrical grid
Clades and clans: a comparison study of two evolutionary models
The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable
arrangements (PDA) model are two binary tree generating models that are widely
used in evolutionary biology. Understanding the distributions of clade sizes
under these two models provides valuable insights into macro-evolutionary
processes, and is important in hypothesis testing and Bayesian analyses in
phylogenetics. Here we show that these distributions are log-convex, which
implies that very large clades or very small clades are more likely to occur
under these two models. Moreover, we prove that there exists a critical value
for each such that for a given clade with size ,
the probability that this clade is contained in a random tree with leaves
generated under the YHK model is higher than that under the PDA model if
, and lower if . Finally, we extend our results
to binary unrooted trees, and obtain similar results for the distributions of
clan sizes.Comment: 21page
Scaling properties of protein family phylogenies
One of the classical questions in evolutionary biology is how evolutionary
processes are coupled at the gene and species level. With this motivation, we
compare the topological properties (mainly the depth scaling, as a
characterization of balance) of a large set of protein phylogenies with a set
of species phylogenies. The comparative analysis shows that both sets of
phylogenies share remarkably similar scaling behavior, suggesting the
universality of branching rules and of the evolutionary processes that drive
biological diversification from gene to species level. In order to explain such
generality, we propose a simple model which allows us to estimate the
proportion of evolvability/robustness needed to approximate the scaling
behavior observed in the phylogenies, highlighting the relevance of the
robustness of a biological system (species or protein) in the scaling
properties of the phylogenetic trees. Thus, the rules that govern the
incapability of a biological system to diversify are equally relevant both at
the gene and at the species level.Comment: Replaced with final published versio
Characterization of Sulfolobus islandicus rod-shaped virus 2 gp19, a single-strand specific endonuclease
The hyperthermophilic Sulfolobus islandicus rod-shaped virus 2 (SIRV2) encodes a 25-kDa protein (SIRV2gp19) annotated as a hypothetical protein with sequence homology to the RecB nuclease superfamily. Even though SIRV2gp19 homologs are conserved throughout the rudivirus family and presumably play a role in the viral life cycle, SIRV2gp19 has not been functionally characterized. To define the minimal requirements for activity, SIRV2gp19 was purified and tested under varying conditions. SIRV2gp19 is a single-strand specific endonuclease that requires Mg2+ for activity and is inactive on double-stranded DNA. A conserved aspartic acid in RecB nuclease superfamily Motif II (D89) is also essential for SIRV2gp19 activity and mutation to alanine (D89A) abolishes activity. Therefore, the SIRV2gp19 cleavage mechanism is similar to previously described RecB nucleases. Finally, SIRV2gp19 single-stranded DNA endonuclease activity could play a role in host chromosome degradation during SIRV2 lytic infection
Caterpillars and fungal pathogens: two co-occurring parasites of an ant-plant mutualism
In mutualisms, each interacting species obtains resources from its partner that it would obtain less efficiently if alone, and so derives a net fitness benefit. In exchange for shelter (domatia) and food, mutualistic plant-ants protect their host myrmecophytes from herbivores, encroaching vines and fungal pathogens. Although selective filters enable myrmecophytes to host those ant species most favorable to their fitness, some insects can by-pass these filters, exploiting the rewards supplied whilst providing nothing in return. This is the case in French Guiana for Cecropia obtusa (Cecropiaceae) as Pseudocabima guianalis caterpillars (Lepidoptera, Pyralidae) can colonize saplings before the installation of their mutualistic Azteca ants. The caterpillars shelter in the domatia and feed on food bodies (FBs) whose production increases as a result. They delay colonization by ants by weaving a silk shield above the youngest trichilium, where the FBs are produced, blocking access to them. This probable temporal priority effect also allows female moths to lay new eggs on trees that already shelter caterpillars, and so to occupy the niche longer and exploit Cecropia resources before colonization by ants. However, once incipient ant colonies are able to develop, they prevent further colonization by the caterpillars. Although no higher herbivory rates were noted, these caterpillars are ineffective in protecting their host trees from a pathogenic fungus, Fusarium moniliforme (Deuteromycetes), that develops on the trichilium in the absence of mutualistic ants. Therefore, the Cecropia treelets can be parasitized by two often overlooked species: the caterpillars that shelter in the domatia and feed on FBs, delaying colonization by mutualistic ants, and the fungal pathogen that develops on old trichilia. The cost of greater FB production plus the presence of the pathogenic fungus likely affect tree growth
On the Bounds of Function Approximations
Within machine learning, the subfield of Neural Architecture Search (NAS) has
recently garnered research attention due to its ability to improve upon
human-designed models. However, the computational requirements for finding an
exact solution to this problem are often intractable, and the design of the
search space still requires manual intervention. In this paper we attempt to
establish a formalized framework from which we can better understand the
computational bounds of NAS in relation to its search space. For this, we first
reformulate the function approximation problem in terms of sequences of
functions, and we call it the Function Approximation (FA) problem; then we show
that it is computationally infeasible to devise a procedure that solves FA for
all functions to zero error, regardless of the search space. We show also that
such error will be minimal if a specific class of functions is present in the
search space. Subsequently, we show that machine learning as a mathematical
problem is a solution strategy for FA, albeit not an effective one, and further
describe a stronger version of this approach: the Approximate Architectural
Search Problem (a-ASP), which is the mathematical equivalent of NAS. We
leverage the framework from this paper and results from the literature to
describe the conditions under which a-ASP can potentially solve FA as well as
an exhaustive search, but in polynomial time.Comment: Accepted as a full paper at ICANN 2019. The final, authenticated
publication will be available at https://doi.org/10.1007/978-3-030-30487-4_3
The InterPro protein families and domains database: 20 years on
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan
Quantum dynamics in strong fluctuating fields
A large number of multifaceted quantum transport processes in molecular
systems and physical nanosystems can be treated in terms of quantum relaxation
processes which couple to one or several fluctuating environments. A thermal
equilibrium environment can conveniently be modelled by a thermal bath of
harmonic oscillators. An archetype situation provides a two-state dissipative
quantum dynamics, commonly known under the label of a spin-boson dynamics. An
interesting and nontrivial physical situation emerges, however, when the
quantum dynamics evolves far away from thermal equilibrium. This occurs, for
example, when a charge transferring medium possesses nonequilibrium degrees of
freedom, or when a strong time-dependent control field is applied externally.
Accordingly, certain parameters of underlying quantum subsystem acquire
stochastic character. Herein, we review the general theoretical framework which
is based on the method of projector operators, yielding the quantum master
equations for systems that are exposed to strong external fields. This allows
one to investigate on a common basis the influence of nonequilibrium
fluctuations and periodic electrical fields on quantum transport processes.
Most importantly, such strong fluctuating fields induce a whole variety of
nonlinear and nonequilibrium phenomena. A characteristic feature of such
dynamics is the absence of thermal (quantum) detailed balance.Comment: review article, Advances in Physics (2005), in pres
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