4,557 research outputs found
Machine learning potentials for complex aqueous made
Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex systems such as solid–liquid interfaces. Here we present a machine learning framework that enables the efficient development and validation of models for complex aqueous systems. Instead of trying to deliver a globally optimal machine learning potential, we propose to develop models applicable to specific thermodynamic state points in a simple and user-friendly process. After an initial ab initio simulation, a machine learning potential is constructed with minimum human effort through a data-driven active learning protocol. Such models can afterward be applied in exhaustive simulations to provide reliable answers for the scientific question at hand or to systematically explore the thermal performance of ab initio methods. We showcase this methodology on a diverse set of aqueous systems comprising bulk water with different ions in solution, water on a titanium dioxide surface, and water confined in nanotubes and between molybdenum disulfide sheets. Highlighting the accuracy of our approach with respect to the underlying ab initio reference, the resulting models are evaluated in detail with an automated validation protocol that includes structural and dynamical properties and the precision of the force prediction of the models. Finally, we demonstrate the capabilities of our approach for the description of water on the rutile titanium dioxide (110) surface to analyze the structure and mobility of water on this surface. Such machine learning models provide a straightforward and uncomplicated but accurate extension of simulation time and length scales for complex systems
Research and Education in Computational Science and Engineering
Over the past two decades the field of computational science and engineering
(CSE) has penetrated both basic and applied research in academia, industry, and
laboratories to advance discovery, optimize systems, support decision-makers,
and educate the scientific and engineering workforce. Informed by centuries of
theory and experiment, CSE performs computational experiments to answer
questions that neither theory nor experiment alone is equipped to answer. CSE
provides scientists and engineers of all persuasions with algorithmic
inventions and software systems that transcend disciplines and scales. Carried
on a wave of digital technology, CSE brings the power of parallelism to bear on
troves of data. Mathematics-based advanced computing has become a prevalent
means of discovery and innovation in essentially all areas of science,
engineering, technology, and society; and the CSE community is at the core of
this transformation. However, a combination of disruptive
developments---including the architectural complexity of extreme-scale
computing, the data revolution that engulfs the planet, and the specialization
required to follow the applications to new frontiers---is redefining the scope
and reach of the CSE endeavor. This report describes the rapid expansion of CSE
and the challenges to sustaining its bold advances. The report also presents
strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie
From Structure to Function in Open Ionic Channels
We consider a simple working hypothesis that all permeation properties of
open ionic channels can be predicted by understanding electrodiffusion in fixed
structures, without invoking conformation changes, or changes in chemical
bonds. We know, of course, that ions can bind to specific protein structures,
and that this binding is not easily described by the traditional electrostatic
equations of physics textbooks, that describe average electric fields, the
so-called `mean field'. The question is which specific properties can be
explained just by mean field electrostatics and which cannot. I believe the
best way to uncover the specific chemical properties of channels is to invoke
them as little as possible, seeking to explain with mean field electrostatics
first. Then, when phenomena appear that cannot be described that way, by the
mean field alone, we turn to chemically specific explanations, seeking the
appropriate tools (of electrochemistry, Langevin, or molecular dynamics, for
example) to understand them. In this spirit, we turn now to the structure of
open ionic channels, apply the laws of electrodiffusion to them, and see how
many of their properties we can predict just that way.Comment: Nearly final version of publicatio
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