scholarly journals Conformational Sampling for Transition State Searches on a Computational Budget

2021 ◽  
Author(s):  
Qiyuan Zhao ◽  
Hsuan-Hao Hsu ◽  
Brett Savoie
Keyword(s):  
Transition State ◽  
Molecular Conformation ◽  
Conformational Space ◽  
Relative Advantage ◽  
Conformational Sampling ◽  
Reaction Prediction ◽  
Computational Budget ◽  
Reacting Systems ◽  
High Level ◽  
The Cost

Transition state searches are the basis for characterizing reaction mechanisms and activation energies, and are thus central to myriad chemical applications. Nevertheless, common search algorithms are sensitive to molecular conformation and the conformational space of even medium-sized reacting systems are too complex to explore with brute force. Here we show that it is possible to train a classifier to learn the features of conformers that conduce successful transition state searches, such that optimal conformers can be down-selected before incurring the cost of a high-level transition state search. To this end, we have benchmarked the use of a modern conformational generation algorithm with our reaction prediction methodology, Yet Another Reaction Program (YARP), for reaction prediction tasks. We demonstrate that neglecting conformer contributions leads to qualitatively incorrect activation energy estimations for a broad range of reactions, whereas a simple random forest classifier can be used to reliably down-select low-barrier conformers. We also compare the relative advantage of performing conformational sampling on reactant, product, and putative transition state geometries. The robust performance of this relatively simple machine learning classifier mitigates cost as a factor when implementing conformational sampling into contemporary reaction prediction workflows.

Changing Role of Agriculture in Income and Employment, and Trends of Agricultural Worker Productivity in Indian States

2020 ◽  
pp. 183-189
Keyword(s):  
Green Revolution ◽  
Positive Trend ◽  
Worker Productivity ◽  
Indian States ◽  
Agricultural Worker ◽  
The Sixties ◽  
High Level ◽  
The Cost ◽  
Changing Role

The productivity of land has been often discussed and deliberated by the academia and policymakers to understand agriculture, however, very few studies have focused on the agriculture worker productivity to analyze this sector. This study concentrates on the productivity of agricultural workers from across the states taking two-time points into consideration. The agriculture worker productivity needs to be dealt with seriously and on a time series basis so that the marginal productivity of worker can be ascertained but also the dependency of worker on agriculture gets revealed. There is still disguised unemployment in all the states and high level of labour migration, yet most of the states showed the dependency has gone down. Although a state like Madhya Pradesh is doing very well in terms of income earned but that is at the cost of increased worker power in agriculture as a result of which, the productivity of worker has gone down. States like Mizoram, Meghalaya, Nagaland and Tripura, though small in size showed remarkable growth in productivity and all these states showed a positive trend in terms of worker shifting away from agriculture. The traditional states which gained the most from Green Revolution of the sixties are performing decently well, but they need to have the next major policy push so that they move to the next orbit of growth.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

scholarly journals Determining the critical period for weed control in high-yielding cotton using common sunflower as a mimic weed

2019 ◽  
Vol 33 (6) ◽  
pp. 800-807 ◽  
Author(s):  
Graham W. Charles ◽  
Brian M. Sindel ◽  
Annette L. Cowie ◽  
Oliver G. G. Knox
Keyword(s):  
Weed Control ◽  
Critical Period ◽  
Yield Loss ◽  
Field Studies ◽  
Growing Degree Days ◽  
Degree Days ◽  
Weed Density ◽  
High Level ◽  
The Cost ◽  
Planting Season

AbstractField studies were conducted over six seasons to determine the critical period for weed control (CPWC) in high-yielding cotton, using common sunflower as a mimic weed. Common sunflower was planted with or after cotton emergence at densities of 1, 2, 5, 10, 20, and 50 plants m−2. Common sunflower was added and removed at approximately 0, 150, 300, 450, 600, 750, and 900 growing degree days (GDD) after planting. Season-long interference resulted in no harvestable cotton at densities of five or more common sunflower plants m−2. High levels of intraspecific and interspecific competition occurred at the highest weed densities, with increases in weed biomass and reductions in crop yield not proportional to the changes in weed density. Using a 5% yield-loss threshold, the CPWC extended from 43 to 615 GDD, and 20 to 1,512 GDD for one and 50 common sunflower plants m−2, respectively. These results highlight the high level of weed control required in high-yielding cotton to ensure crop losses do not exceed the cost of control.

scholarly journals Computing the Exact Number of Similarity Classes in the Longest Edge Bisection of Tetrahedra

Mathematics ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1447
Author(s):  
Jose P. Suárez ◽  
Agustín Trujillo ◽  
Tania Moreno
Keyword(s):  
Data Structure ◽  
Stability Condition ◽  
Open Problem ◽  
Integer Arithmetic ◽  
Exact Number ◽  
Similarity Class ◽  
The Stability ◽  
High Level ◽  
The Cost

Showing whether the longest-edge (LE) bisection of tetrahedra meshes degenerates the stability condition or not is still an open problem. Some reasons, in part, are due to the cost for achieving the computation of similarity classes of millions of tetrahedra. We prove the existence of tetrahedra where the LE bisection introduces, at most, 37 similarity classes. This family of new tetrahedra was roughly pointed out by Adler in 1983. However, as far as we know, there has been no evidence confirming its existence. We also introduce a new data structure and algorithm for computing the number of similarity tetrahedral classes based on integer arithmetic, storing only the square of edges. The algorithm lets us perform compact and efficient high-level similarity class computations with a cost that is only dependent on the number of similarity classes.

One-IPC high-level simulation of microthreaded many-core architectures

2016 ◽  
Vol 31 (2) ◽  
pp. 152-162 ◽  
Author(s):  
Irfan Uddin
Keyword(s):  
Design Space Exploration ◽  
Instruction Set ◽  
Efficient Design ◽  
Simulation Framework ◽  
Fine Grained ◽  
Detailed Simulation ◽  
High Level ◽  
Many Core ◽  
The Cost ◽  
Multiple Clusters

The microthreaded many-core architecture is comprised of multiple clusters of fine-grained multi-threaded cores. The management of concurrency is supported in the instruction set architecture of the cores and the computational work in application is asynchronously delegated to different clusters of cores, where the cluster is allocated dynamically. Computer architects are always interested in analyzing the complex interaction amongst the dynamically allocated resources. Generally a detailed simulation with a cycle-accurate simulation of the execution time is used. However, the cycle-accurate simulator for the microthreaded architecture executes at the rate of 100,000 instructions per second, divided over the number of simulated cores. This means that the evaluation of a complex application executing on a contemporary multi-core machine can be very slow. To perform efficient design space exploration we present a co-simulation environment, where the detailed execution of instructions in the pipeline of microthreaded cores and the interactions amongst the hardware components are abstracted. We present the evaluation of the high-level simulation framework against the cycle-accurate simulation framework. The results show that the high-level simulator is faster and less complicated than the cycle-accurate simulator but with the cost of losing accuracy.

Criteria for the Evaluation of Social Policy Effectiveness of States

2014 ◽  
pp. 87-97
Author(s):  
V. Sautkina
Keyword(s):  
Developed Countries ◽  
Legal Aspects ◽  
Educational Services ◽  
State Control ◽  
National Education ◽  
Current State ◽  
The Usa ◽  
The Government ◽  
High Level ◽  
The Cost

The following article is devoted to the study of current state of national education and healthcare systems. The cost of services in these areas constantly increases, there for even developed countries are forced to make significant efforts in order to maintain earlier achieved results. Due to this reason countries entered into the period of constant reforms with the purpose of maintaining that high level of health and educational services for all segments of population with a constant reduction of its volume of financing. The legal aspects of these changes are requiring manifestation of the will of politicians in order to overcome the opposition of parties which are defending their interests. As an example, the main opponents of the healthcare reforms proposed by Barak Obama in the USA are Republicans who are concerned about a significant increase of a state control over the entire national insurance system. The author comes to the conclusion that only joint actions of the government and every segment of population might actually improve the quality of medical and educational services.

Cost Effectiveness Analysis in Short Sea Shipping: Evidence from Northeast Asian Routes

2021 ◽  
Vol 9 (12) ◽  
pp. 1340
Author(s):  
Xue-Bin Zheng ◽  
Yul-Seong Kim ◽  
Young-Ran Shin
Keyword(s):  
Supply Chain ◽  
Cost Effectiveness ◽  
Short Sea Shipping ◽  
Effectiveness Analysis ◽  
Transportation Modes ◽  
Lift Off ◽  
Cooperative Relationship ◽  
High Level ◽  
Northeast Asian ◽  
The Cost

Nowadays, roll-on/roll-off (Ro-Ro) is an important mode for short sea shipping (SSS) due to its advantages of fast and convenient load and unloading system. Despite the advantages, the market share of Ro-Ro is insignificant compared with lift-on/lift-off (Lo-Lo) in the Northeast Asian region that is geographically suitable for fostering SSS. Therefore, it is of utmost importance to have a better understanding of the effectiveness or Ro-Ro and Lo-Lo in the regional SSS market. For this purpose, this paper develops a model to estimate the total logistics cost of the two transportation modes. The total logistics costs of Ro-Ro and Lo-Lo are calculated on three major SSS routes between Korea and Japan. The results show that Lo-Lo outperforms Ro-Ro on most routes in terms of the cost effectiveness, and Ro-Ro is competitive only for high-priced and time-sensitive cargo. However, it is also documented that Ro-Ro transport has a significant impact on reduction in the total logistics costs when companies integrate the supply chain and improve the cooperative relationship to a high level.

Smartphone Adoption on Fruit Marketing Communication: a Traders Perception

2020 ◽  
Vol 19 (2) ◽  
pp. 433-446
Author(s):  
Heri Akhmadi ◽  
Muhammad Fauzan
Keyword(s):  
Descriptive Analysis ◽  
Low Complexity ◽  
Ease Of Use ◽  
Relative Advantage ◽  
Marketing Communication ◽  
Communication Tool ◽  
Marketing Activities ◽  
High Level ◽  
Media Applications ◽  
Yogyakarta City

Smartphone is one of the information technology devices that widely used by traders in marketing activities. Aside from being a communication tool, traders also utilize smartphones to obtain market information and communicate about products and services to consumers. This study aims to analyze profile and perceptions of fruit traders in using smartphones as a marketing communication tool. This research employed quantitative method and descriptive analysis using five point Likert scale to examine  the  perception of fruit traders in Yogyakarta City. The results revealed that traders adopted smartphones on fruit marketing communication due to it perceived to provide a relative advantage, with a high level of ease of use, visible benefits, and low complexity and risk. Furthermore, Samsung, Telkomsel, and WhatsApp were brands of smartphones, telecommunications providers, and social media applications mostly chose by traders.

Application of transfer pricing as a management accounting tool in the project management system

2021 ◽  
pp. 43-53
Author(s):  
N. P. Agafonova
Keyword(s):  
Project Management ◽  
Management Accounting ◽  
Transfer Pricing ◽  
Information Support ◽  
Sufficient Information ◽  
Project Management System ◽  
Management Concept ◽  
Modern Economic ◽  
High Level ◽  
The Cost

Modern economic conditions, due to the high level of competition, lead to the need to search for internal reserves to improve the efficiency of economic entities, one of the solutions to this problem can be considered the application of the management concept “project management”. However, its full implementation is impossible without sufficient information support, which is eliminated as a result of the use of various management accounting tools, one of which is transfer pricing. The article presents the results of a study on the use of transfer education in determining the cost of implementing an agricultural project.

scholarly journals Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank

2018 ◽  
Vol 19 (11) ◽  
pp. 3405 ◽  
Author(s):  
Emanuel Peter ◽  
Jiří Černý
Keyword(s):  
Partition Function ◽  
Protein Data Bank ◽  
Protein Structures ◽  
Data Bank ◽  
Weighting Factor ◽  
Potential Of Mean Force ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Conformational Sampling ◽  
Speed Increase

In this article, we present a method for the enhanced molecular dynamics simulation of protein and DNA systems called potential of mean force (PMF)-enriched sampling. The method uses partitions derived from the potentials of mean force, which we determined from DNA and protein structures in the Protein Data Bank (PDB). We define a partition function from a set of PDB-derived PMFs, which efficiently compensates for the error introduced by the assumption of a homogeneous partition function from the PDB datasets. The bias based on the PDB-derived partitions is added in the form of a hybrid Hamiltonian using a renormalization method, which adds the PMF-enriched gradient to the system depending on a linear weighting factor and the underlying force field. We validated the method using simulations of dialanine, the folding of TrpCage, and the conformational sampling of the Dickerson–Drew DNA dodecamer. Our results show the potential for the PMF-enriched simulation technique to enrich the conformational space of biomolecules along their order parameters, while we also observe a considerable speed increase in the sampling by factors ranging from 13.1 to 82. The novel method can effectively be combined with enhanced sampling or coarse-graining methods to enrich conformational sampling with a partition derived from the PDB.

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