1,707 research outputs found
Identifying Structure Transitions Using Machine Learning Methods
Methodologies from data science and machine learning, both new and old, provide an exciting opportunity to investigate physical systems using extremely expressive statistical modeling techniques. Physical transitions are of particular interest, as they are accompanied by pattern changes in the configurations of the systems. Detecting and characterizing pattern changes in data happens to be a particular strength of statistical modeling in data science, especially with the highly expressive and flexible neural network models that have become increasingly computationally accessible in recent years through performance improvements in both hardware and algorithmic implementations. Conceptually, the machine learning approach can be regarded as one that employing algorithms that eschew explicit instructions in favor of strategies based around pattern extraction and inference driven by statistical analysis and large complex data sets. This allows for the investigation of physical systems using only raw configurational information to make inferences instead of relying on physical information obtained from a priori knowledge of the system. This work focuses on the extraction of useful compressed representations of physical configurations from systems of interest to automate phase classification tasks in addition to the identification of critical points and crossover regions
Potentials of mean force in acidic proton transfer reactions in constrained geometries
Free energy barriers associated with the transfer of an excess proton in water and related to the potentials of mean force in proton transfer episodes have been computed in a wide range of thermodynamic states, from low-density amorphous ices to high-temperature liquids under the critical point for unconstrained and constrained systems. The latter were represented by set-ups placed inside hydrophobic graphene slabs at the nanometric scale allocating a few water layers, namely one or two in the narrowest case. Water–proton and carbon–proton forces were modelled with a Multi-State Empirical Valence Bond method. As a general trend, a competition between the effects of confinement and temperature is observed on the local hydrogen-bonded structures around the lone proton and, consequently, on the mean force exerted by its environment on the water molecule carrying the proton. Free energy barriers estimated from the computed potentials of mean force tend to rise with the combined effect of increasing temperatures and the packing effect due to a larger extent of hydrophobic confinement. The main reason observed for such enhancement of the free energy barriers was the breaking of the second coordination shell around the lone proton.Postprint (author's final draft
Surrogate Model-Based Strategy for Cryogenic Cavitation Model Validation and Sensitivity Evaluation
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/76195/1/AIAA-2006-5047-399.pd
Tiling solutions for optimal biological sensing
Biological systems, from cells to organisms, must respond to the ever
changing environment in order to survive and function. This is not a simple
task given the often random nature of the signals they receive, as well as the
intrinsically stochastic, many body and often self-organized nature of the
processes that control their sensing and response and limited resources.
Despite a wide range of scales and functions that can be observed in the living
world, some common principles that govern the behavior of biological systems
emerge. Here I review two examples of very different biological problems:
information transmission in gene regulatory networks and diversity of adaptive
immune receptor repertoires that protect us from pathogens. I discuss the
trade-offs that physical laws impose on these systems and show that the optimal
designs of both immune repertoires and gene regulatory networks display similar
discrete tiling structures. These solutions rely on locally non-overlapping
placements of the responding elements (genes and receptors) that, overall,
cover space nearly uniformly.Comment: 11 page
Predicting electronic structures at any length scale with machine learning
The properties of electrons in matter are of fundamental importance. They
give rise to virtually all molecular and material properties and determine the
physics at play in objects ranging from semiconductor devices to the interior
of giant gas planets. Modeling and simulation of such diverse applications rely
primarily on density functional theory (DFT), which has become the principal
method for predicting the electronic structure of matter. While DFT
calculations have proven to be very useful to the point of being recognized
with a Nobel prize in 1998, their computational scaling limits them to small
systems. We have developed a machine learning framework for predicting the
electronic structure on any length scale. It shows up to three orders of
magnitude speedup on systems where DFT is tractable and, more importantly,
enables predictions on scales where DFT calculations are infeasible. Our work
demonstrates how machine learning circumvents a long-standing computational
bottleneck and advances science to frontiers intractable with any current
solutions. This unprecedented modeling capability opens up an inexhaustible
range of applications in astrophysics, novel materials discovery, and energy
solutions for a sustainable future
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