Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis

Given the piecewise approach to modeling intermolecular interactions for force fields, they can be difficult to parameterize since they are fit to data like total energies that only indirectly connect to their separable functional forms. Furthermore, by neglecting certain types of molecular interactions such as charge penetration and charge transfer, most classical force fields must rely on, but do not always demonstrate, how cancellation of errors occurs among the remaining molecular interactions accounted for such as exchange repulsion, electrostatics, and polarization. In this work we present the first generation of the (many-body) MB-UCB force field that explicitly accounts for the decomposed molecular interactions commensurate with a variational energy decomposition analysis, including charge transfer, with force field design choices that reduce the computational expense of the MB-UCB potential while remaining accurate. We optimize parameters using only single water molecule and water cluster data up through pentamers, with no fitting to condensed phase data, and we demonstrate that high accuracy is maintained when the force field is subsequently validated against conformational energies of larger water cluster data sets, radial distribution functions of the liquid phase, and the temperature dependence of thermodynamic and transport water properties. We conclude that MB-UCB is comparable in performance to MB-Pol, but is less expensive and more transferable by eliminating the need to represent short-ranged interactions through large parameter fits to high order polynomials

copulaedas: An R Package for Estimation of Distribution Algorithms Based on Copulas

The use of copula-based models in EDAs (estimation of distribution algorithms) is currently an active area of research. In this context, the copulaedas package for R provides a platform where EDAs based on copulas can be implemented and studied. The package offers complete implementations of various EDAs based on copulas and vines, a group of well-known optimization problems, and utility functions to study the performance of the algorithms. Newly developed EDAs can be easily integrated into the package by extending an S4 class with generic functions for their main components. This paper presents copulaedas by providing an overview of EDAs based on copulas, a description of the implementation of the package, and an illustration of its use through examples. The examples include running the EDAs defined in the package, implementing new algorithms, and performing an empirical study to compare the behavior of different algorithms on benchmark functions and a real-world problem

Research in computer science

Several short summaries of the work performed during this reporting period are presented. Topics discussed in this document include: (1) resilient seeded errors via simple techniques; (2) knowledge representation for engineering design; (3) analysis of faults in a multiversion software experiment; (4) implementation of parallel programming environment; (5) symbolic execution of concurrent programs; (6) two computer graphics systems for visualization of pressure distribution and convective density particles; (7) design of a source code management system; (8) vectorizing incomplete conjugate gradient on the Cyber 203/205; (9) extensions of domain testing theory and; (10) performance analyzer for the pisces system

Analog and Mixed Signal Verification

More and more electronic systems have components that are not purely digital. Verification of such systems is a much less developed discipline than the digital equivalents and the application of formal (mathematically complete) techniques is a nascent area. In this paper, we will discuss the nature of analog circuit design and describe the way verification is done in practice today. We will describe some “formal” approaches coming from the analog design community. We will describe some of the approaches to formal verification that have been presented in recent literature. Finally, we will mention some areas where there are opportunities for future work

What Should EDA Fund? Developing a Model for Pre-Assessment of Economic Development Investments

This paper describes the completion of a “comprehensive study of regionalism” that was conducted by a joint team of economists and economic development specialists for the Economic Development Administration (EDA). The project consisted of two main activities: an examination of the factors associated with economic development success and the creation of a practical interactive tool for EDA project assessment and comparison. Findings from surveys, interviews, and project case studies are discussed in terms of their support for a positive relationship between successful economic development efforts and factors such as leadership and private investment. Also, the authors discuss the creation of a quantitative assessment model utilizing well-known approaches such as economic impact multipliers and cluster theory. The primary contribution of this work to the existing body of EDA-focused research and evaluation literature is introducing a means of using standardized scores, also known as z-scores, to compare and assess economic development projects across both industries and regions.regional economic development, economic impact, assessment model, EDA, z-score