3 research outputs found
Machine Learning Topological Invariants with Neural Networks
In this Letter we supervisedly train neural networks to distinguish different
topological phases in the context of topological band insulators. After
training with Hamiltonians of one-dimensional insulators with chiral symmetry,
the neural network can predict their topological winding numbers with nearly
100% accuracy, even for Hamiltonians with larger winding numbers that are not
included in the training data. These results show a remarkable success that the
neural network can capture the global and nonlinear topological features of
quantum phases from local inputs. By opening up the neural network, we confirm
that the network does learn the discrete version of the winding number formula.
We also make a couple of remarks regarding the role of the symmetry and the
opposite effect of regularization techniques when applying machine learning to
physical systems.Comment: 6 pages, 4 figures and 1 table + 2 pages of supplemental materia
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Photoelectron Transfer Dissociation Reveals Surprising Favorability of Zwitterionic States in Large Gaseous Peptides and Proteins
Structural
characterization of proteins in the gas phase is becoming
increasingly popular, highlighting the need for a greater understanding
of how proteins behave in the absence of solvent. It is clear that
charged residues exert significant influence over structures in the
gas phase due to strong Coulombic and hydrogen-bonding interactions.
The net charge for a gaseous ion is easily identified by mass spectrometry,
but the presence of zwitterionic pairs or salt bridges has previously
been more difficult to detect. We show that these sites can be revealed
by photoinduced electron transfer dissociation, which produces characteristic
c and z ions only if zwitterionic species are present. Although previous
work on small molecules has shown that zwitterionic pairs are rarely
stable in the gas phase, we now demonstrate that charge-separated
states are favored in larger molecules. Indeed, we have detected zwitterionic
pairs in peptides and proteins where the net charge equals the number
of basic sites, requiring additional protonation at nonbasic residues.
For example, the small protein ubiquitin can sustain a zwitterionic
conformer for all charge states up to 14+, despite having only 13
basic sites. Virtually all of the peptides/proteins examined herein
contain zwitterionic sites if both acidic and basic residues are present
and the overall charge density is low. This bias in favor of charge-separated
states has important consequences for efforts to model gaseous proteins
via computational analysis, which should consider not only charge
state isomers that include salt bridges but also protonation at nonbasic
residues