emgr - The Empirical Gramian Framework

System Gramian matrices are a well-known encoding for properties of input-output systems such as controllability, observability or minimality. These so-called system Gramians were developed in linear system theory for applications such as model order reduction of control systems. Empirical Gramian are an extension to the system Gramians for parametric and nonlinear systems as well as a data-driven method of computation. The empirical Gramian framework - emgr - implements the empirical Gramians in a uniform and configurable manner, with applications such as Gramian-based (nonlinear) model reduction, decentralized control, sensitivity analysis, parameter identification and combined state and parameter reduction

Tensor network method for reversible classical computation

We develop a tensor network technique that can solve universal reversible classical computational problems, formulated as vertex models on a square lattice [Nat. Commun. 8, 15303 (2017)]. By encoding the truth table of each vertex constraint in a tensor, the total number of solutions compatible with partial inputs and outputs at the boundary can be represented as the full contraction of a tensor network. We introduce an iterative compression-decimation (ICD) scheme that performs this contraction efficiently. The ICD algorithm first propagates local constraints to longer ranges via repeated contraction-decomposition sweeps over all lattice bonds, thus achieving compression on a given length scale. It then decimates the lattice via coarse-graining tensor contractions. Repeated iterations of these two steps gradually collapse the tensor network and ultimately yield the exact tensor trace for large systems, without the need for manual control of tensor dimensions. Our protocol allows us to obtain the exact number of solutions for computations where a naive enumeration would take astronomically long times.We thank Justin Reyes, Oskar Pfeffer, and Lei Zhang for many useful discussions. The computations were carried out at Boston University's Shared Computing Cluster. We acknowledge the Condensed Matter Theory Visitors Program at Boston University for support. Z.-C. Y. and C. C. are supported by DOE Grant No. DE-FG02-06ER46316. E.R.M. is supported by NSF Grant No. CCF-1525943. (Condensed Matter Theory Visitors Program at Boston University; DE-FG02-06ER46316 - DOE; CCF-1525943 - NSF)Accepted manuscrip

Building “with the systems” vs. building “in the system” of IMS open technology of prefabricated construction: challenges for new “infill” industry for massive housing retrofitting

Post-war industrialized housing between 1955 and 1985 in Belgrade and its special form of integrated prefabrication has been analyzed with a strong interest in transformation capacity of industrialized building model (IBM) on different technical levels. Research field is massive housing up to 23 floors, 400 dwellings per building and different housing layouts—to be evaluated for potential retrofitting at the dwelling level. IBM for massive housing built with IMS construction technology represents an integration of systems’ components into hierarchy assemblies by simple joints. IMS Building Technology by IMS Institute is the system for high-rise structures with prefabricated elements of the skeleton. In order to assess the current situation regarding the selection and implementation of energy savings measures and the role of industrialized technology in supporting the rehabilitation of post-war housing in Belgrade—building configuration model and IMS construction technology has been analyzed, providing in-depth information on the way building components and systems are put together into IBM. In which way retrofit may be approached? IBM is represented with graph model (GM) diagram to describe a number of value-added processes according to independent systems/components and flexible connections. This paper highlights the technological aspects of “open” prefabrication industry and building with the systems that should be assessed in the future retrofitting of massive housing based on industrialization and energy efficiency. The paper proposes an IBM that provides concrete description of massive housing buildings, the requirements for information to be provided to approving refurbishment processes. The research also addresses both: challenges as well as opportunities for advancing Building Information Modeling (BIM) standards in off-site re-construction of massive housing with new “infill” industry.Peer ReviewedPostprint (published version

RNA-RNA interaction prediction based on multiple sequence alignments

Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both thermodynamic stability and sequence covariation. We present the \emph{a priori} folding algorithm \texttt{ripalign}, whose input consists of two (given) multiple sequence alignments (MSA). \texttt{ripalign} outputs (1) the partition function, (2) base-pairing probabilities, (3) hybrid probabilities and (4) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm \texttt{rip}, \texttt{ripalign} requires negligible additional memory resource. Furthermore, we incorporate possible structure constraints as input parameters into our algorithm. The algorithm described here is implemented in C as part of the \texttt{rip} package. The supplemental material, source code and input/output files can freely be downloaded from \url{http://www.combinatorics.cn/cbpc/ripalign.html}. \section{Contact} Christian Reidys \texttt{[email protected]}Comment: 8 pages, 9 figure