Node balanced steady states: Unifying and generalizing complex and detailed balanced steady states

We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we introduce a graph, called a reaction graph, that has one edge for each reaction but potentially multiple nodes for each complex. A special class of steady states, called node balanced steady states, is naturally associated with such a reaction graph. We show that complex and detailed balanced steady states are special cases of node balanced steady states by choosing appropriate reaction graphs. Further, we show that node balanced steady states have properties analogous to complex balanced steady states, such as uniqueness and asymptotic stability in each stoichiometric compatibility class. Moreover, we associate an integer, called the deficiency, to a reaction graph that gives the number of independent relations in the reaction rate constants that need to be satisfied for a positive node balanced steady state to exist. The set of reaction graphs (modulo isomorphism) is equipped with a partial order that has the complex balanced reaction graph as minimal element. We relate this order to the deficiency and to the set of reaction rate constants for which a positive node balanced steady state exists

Addition of flow reactions preserving multistationarity and bistability

We consider the question whether a chemical reaction network preserves the number and stability of its positive steady states upon inclusion of inflow and outflow reactions. Often a model of a reaction network is presented without inflows and outflows, while in fact some of the species might be degraded or leaked to the environment, or be synthesized or transported into the system. We provide a sufficient and easy-to-check criterion based on the stoichiometry of the reaction network alone and discuss examples from systems biology

Activation Energy of Hydrogen Adsorption on Pt(111) in Alkaline Media: An Impedance Spectroscopy Study at Variable Temperatures

The hydrogen evolution reaction is one of the most studied processes in electrochemistry, and platinum is by far the best catalyst for this reaction. Despite the importance of this reaction on platinum, detailed and accurate kinetic measurements of the steps that lead to the main reaction are still lacking, particularly because of the fast rate of the reaction. Hydrogen adsorption on Pt(111) has been taken as a benchmark system in a large number of computational studies, but reliable experimental data to compare with the computational studies is very scarce. To gain further knowledge on this matter, a temperature study of the hydrogen adsorption reaction has been carried out to obtain kinetic information for this process on Pt(111) in alkaline solution. This was achieved by measuring electrochemical impedance spectra and cyclic voltammograms in the range of 278 ≤ T ≤ 318 (K) to obtain the corresponding surface coverage by adsorbed species and the faradaic charge transfer resistance. From this data, the standard rate constant has been extracted with a kinetic model assuming a Frumkin-type isotherm, resulting in values of 2.60 × 10–7 ≤ k0 ≤ 1.68 × 10–6 (s–1). The Arrehnius plot gives an activation energy of 32 kJ mol–1. Comparisons are made with values calculated by computational methods and reported values for the overall HER, giving a reference frame to support future studies on hydrogen catalysis.This work was financially supported by the MINECO (Spain) project no. CTQ2016-76221-P. L.E.B. thanks the Generalitat Valenciana for funding from the Santiago Grisolia Program (no. GRISOLIAP/2017/181)

SYNPA: SMT Performance Analysis and Allocation of Threads to Cores in ARM Processors

Simultaneous multithreading processors improve throughput over single-threaded processors thanks to sharing internal core resources among instructions from distinct threads. However, resource sharing introduces inter-thread interference within the core, which has a negative impact on individual application performance and can significantly increase the turnaround time of multi-program workloads. The severity of the interference effects depends on the competing co-runners sharing the core. Thus, it can be mitigated by applying a thread-to-core allocation policy that smartly selects applications to be run in the same core to minimize their interference. This paper presents SYNPA, a simple approach that dynamically allocates threads to cores in an SMT processor based on their run-time dynamic behavior. The approach uses a regression model to select synergistic pairs to mitigate intra-core interference. The main novelty of SYNPA is that it uses just three variables collected from the performance counters available in current ARM processors at the dispatch stage. Experimental results show that SYNPA outperforms the default Linux scheduler by around 36%, on average, in terms of turnaround time in 8-application workloads combining frontend bound and backend bound benchmarks.Comment: 11 pages, 9 figure

CELLO: Compiler-Assisted Efficient Load-Load Ordering in Data-Race-Free Regions

Efficient Total Store Order (TSO) implementations allow loads to execute speculatively out-of-order. To detect order violations, the load queue (LQ) holds all the in-flight loads and is searched on every invalidation and cache eviction. Moreover, in a simultaneous multithreading processor (SMT), stores also search the LQ when writing to cache. LQ searches entail considerable energy consumption. Furthermore, the processor stalls upon encountering the LQ full or when its ports are busy. Hence, the LQ is a critical structure in terms of both energy and performance. In this work, we observe that the use of the LQ could be dramatically optimized under the guarantees of the datarace-free (DRF) property imposed by modern programming languages. To leverage this observation, we propose CELLO, a software-hardware co-design in which the compiler detects memory operations in DRF regions and the hardware optimizes their execution by safely skipping LQ searches without violating the TSO consistency model. Furthermore, CELLO allows removing DRF loads from the LQ earlier, as they do not need to be searched to detect consistency violations. With minimal hardware overhead, we show that an 8-core 2- way SMT processor with CELLO avoids almost all conservative searches to the LQ and significantly reduces its occupancy. CELLO allows i) to reduce the LQ energy expenditure by 33% on average (up to 53%) while performing 2.8% better on average (up to 18.6%) than the baseline system, and ii) to shrink the LQ size from 192 to only 80 entries, reducing the LQ energy expenditure as much as 69% while performing on par with a mainstream LQ implementation

Phosphate sink containing two-component signaling systems as tunable threshold devices.

Published onlineJournal ArticleResearch Support, Non-U.S. Gov'tSynthetic biology aims to design de novo biological systems and reengineer existing ones. These efforts have mostly focused on transcriptional circuits, with reengineering of signaling circuits hampered by limited understanding of their systems dynamics and experimental challenges. Bacterial two-component signaling systems offer a rich diversity of sensory systems that are built around a core phosphotransfer reaction between histidine kinases and their output response regulator proteins, and thus are a good target for reengineering through synthetic biology. Here, we explore the signal-response relationship arising from a specific motif found in two-component signaling. In this motif, a single histidine kinase (HK) phosphotransfers reversibly to two separate output response regulator (RR) proteins. We show that, under the experimentally observed parameters from bacteria and yeast, this motif not only allows rapid signal termination, whereby one of the RRs acts as a phosphate sink towards the other RR (i.e. the output RR), but also implements a sigmoidal signal-response relationship. We identify two mathematical conditions on system parameters that are necessary for sigmoidal signal-response relationships and define key parameters that control threshold levels and sensitivity of the signal-response curve. We confirm these findings experimentally, by in vitro reconstitution of the one HK-two RR motif found in the Sinorhizobium meliloti chemotaxis pathway and measuring the resulting signal-response curve. We find that the level of sigmoidality in this system can be experimentally controlled by the presence of the sink RR, and also through an auxiliary protein that is shown to bind to the HK (yielding Hill coefficients of above 7). These findings show that the one HK-two RR motif allows bacteria and yeast to implement tunable switch-like signal processing and provides an ideal basis for developing threshold devices for synthetic biology applications.Exeter University Science Strateg