@article{10664,
  abstract     = {Since the discovery of correlated insulators and superconductivity in magic-angle twisted bilayer graphene (tBLG) ([1, 2], JCCM April 2018), theorists have been excitedly pursuing the alluring mix of band topology, symmetry breaking, Mott insulators and superconductivity at play, as well as the potential relation (if any) to high-Tc physics. Now a new stream
of experimental work is arriving which further enriches the story. To briefly recap Episodes 1 and 2 (JCCM April and November 2018), when two graphene layers are stacked with a small rotational mismatch θ, the resulting long-wavelength moire pattern leads to a superlattice potential which reconstructs the low energy band structure. When θ approaches the “magic-angle” θM ∼ 1 ◦, the band structure features eight nearly-flat bands which fill when the electron number per moire unit cell, n/n0, lies between −4 < n/n0 < 4. The bands can be counted as 8 = 2 × 2 × 2: for each spin (2×) and valley (2×) characteristic of monolayergraphene, tBLG has has 2× flat bands which cross at mini-Dirac points.},
  author       = {Yankowitz, Mathew and Chen, Shaowen and Polshyn, Hryhoriy and Watanabe, K. and Taniguchi, T. and Graf, David and Young, Andrea F. and Dean, Cory R. and Sharpe, Aaron L. and Fox, E.J. and Barnard, A.W. and Finney, Joe},
  journal      = {Journal Club for Condensed Matter Physics},
  publisher    = {Simons Foundation ; University of California, Riverside},
  title        = {{New correlated phenomena in magic-angle twisted bilayer graphene/s}},
  doi          = {10.36471/jccm_february_2019_03},
  volume       = {03},
  year         = {2019},
}

@inproceedings{10722,
  abstract     = {Bilayer graphene, rotationally faulted to ~1.1 degree misalignment, has recently been shown to host superconducting and resistive states associated with the formation of a flat electronic band. While numerous theories exist for the origins of both states, direct validation of these theories remains an outstanding experimental problem. Here, we focus on the resistive states occurring at commensurate filling (1/2, 1/4, and 3/4) of the two lowest superlattice bands. We test theoretical proposals that these states arise due to broken spin—and/or valley—symmetry by performing direct magnetic imaging with nanoscale SQUID-on-tip microscopy. This technique provides single-spin resolved magnetometry on sub-100nm length scales. I will present imaging data from our 4.2K nSOT microscope on graphite-gated twisted bilayers near the flat band condition and discuss the implications for the physics of the commensurate resistive states.},
  author       = {Serlin, Marec and Tschirhart, Charles and Polshyn, Hryhoriy and Zhu, Jiacheng and Huber, Martin E. and Young, Andrea},
  booktitle    = {APS March Meeting 2019},
  issn         = {0003-0503},
  location     = {Boston, MA, United States},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy}},
  volume       = {64},
  year         = {2019},
}

@inproceedings{10723,
  abstract     = {In monolayer graphene, the interplay of electronic correlations with the internal spin- and valley- degrees of freedom leads to a complex phase diagram of isospin symmetry breaking at high magnetic fields. Recently, Wei et al. (Science (2018)) demonstrated that spin waves can be electrically generated and detected in graphene heterojunctions, allowing direct experiment access to the spin degree of freedom. Here, we apply this technique to high quality graphite-gated graphene devices showing robust fractional quantum Hall phases and isospin phase transitions. We use an edgeless Corbino geometry to eliminate the contributions of edge states to the spin-wave mediated nonlocal voltage, allowing unambiguous identification of spin wave transport signatures. Our data reveal two phases within the ν = 1 plateau. For exactly ν=1, charge is localized but spin waves propagate freely while small carrier doping completely quenches the low-energy spin-wave transport, even as those charges remain localized. We identify this new phase as a spin textured electron solid. We also find that spin-wave transport is modulated by phase transitions in the valley order that preserve spin polarization, suggesting that this technique is sensitive to both spin and valley order.},
  author       = {Zhou, Haoxin and Polshyn, Hryhoriy and Tanaguchi, Takashi and Watanabe, Kenji and Young, Andrea},
  booktitle    = {APS March Meeting 2019},
  issn         = {0003-0503},
  location     = {Boston, MA, United States},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Spin wave transport through electron solids and fractional quantum Hall liquids in graphene}},
  volume       = {64},
  year         = {2019},
}

@inproceedings{10724,
  abstract     = {Twisted bilayer graphene (tBLG) near the flat band condition is a versatile new platform for the study of correlated physics in 2D. Resistive states have been observed at several commensurate fillings of the flat miniband, along with superconducting states near half filling. To better understand the electronic structure of this system, we study electronic transport of graphite gated superconducting tBLG devices in the normal regime. At high magnetic fields, we observe full lifting of the spin and valley degeneracy. The transitions in the splitting of this four-fold degeneracy as a function of carrier density indicate Landau level (LL) crossings, which tilted field measurements show occur between LLs with different valley polarization. Similar LL structure measured in two devices, one with twist angle θ=1.08° at ambient pressure and one at θ=1.27° and 1.33GPa, suggests that the dimensionless combination of twist angle and interlayer coupling controls the relevant details of the band structure. In addition, we find that the temperature dependence of the resistance at B=0 shows linear growth at several hundred Ohm/K in a broad range of temperatures. We discuss the implications for modeling the scattering processes in this system.},
  author       = {Polshyn, Hryhoriy and Zhang, Yuxuan and Yankowitz, Matthew and Chen, Shaowen and Taniguchi, Takashi and Watanabe, Kenji and Graf, David E. and Dean, Cory R. and Young, Andrea},
  booktitle    = {APS March Meeting 2019},
  issn         = {0003-0503},
  location     = {Boston, MA, United States},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Normal state transport in superconducting twisted bilayer graphene}},
  volume       = {64},
  year         = {2019},
}

@inproceedings{10725,
  abstract     = {Bilayer graphene with ~ 1.1 degrees twist mismatch between the layers hosts a low energy flat band in which the Coulomb interaction is large relative to the bandwidth, promoting correlated insulating states at half band filling, and superconducting (SC) phases with dome-like structure neighboring correlated insulating states. Here we show measurements of a dual-graphite-gated twisted bilayer graphene device, which minimizes charge inhomogeneity. We observe new correlated phases, including for the first time a SC pocket near half-filling of the electron-doped band and resistive states at quarter-filling of both bands that emerge in a magnetic field. Changing the layer polarization with vertical electric field reveals an unexpected competition between SC and correlated insulator phases, which we interpret to result from differences in disorder of each graphene layer and underscores the spatial inhomogeneity like twist angle as a significant source of disorder in these devices [1].},
  author       = {Chen, Shaowen and Yankowitz, Matthew and Polshyn, Hryhoriy and Watanabe, Kenji and Taniguchi, Takashi and Graf, David E. and Young, Andrea and Dean, Cory R.},
  booktitle    = {APS March Meeting 2019},
  issn         = {0003-0503},
  location     = {Boston, MA, United States},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Correlated insulating and superconducting phases in twisted bilayer graphene}},
  volume       = {64},
  year         = {2019},
}

@article{9460,
  abstract     = {Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.},
  author       = {Kim, M. Yvonne and Ono, Akemi and Scholten, Stefan and Kinoshita, Tetsu and Zilberman, Daniel and Okamoto, Takashi and Fischer, Robert L.},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  keywords     = {Multidisciplinary},
  number       = {19},
  pages        = {9652--9657},
  publisher    = {National Academy of Sciences},
  title        = {{DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm}},
  doi          = {10.1073/pnas.1821435116},
  volume       = {116},
  year         = {2019},
}

@article{9530,
  abstract     = {Background
DNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.

Results
Our data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.

Conclusions
Based on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.},
  author       = {Harris, Keith D. and Lloyd, James P. B. and Domb, Katherine and Zilberman, Daniel and Zemach, Assaf},
  issn         = {1756-8935},
  journal      = {Epigenetics and Chromatin},
  publisher    = {Springer Nature},
  title        = {{DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development}},
  doi          = {10.1186/s13072-019-0307-4},
  volume       = {12},
  year         = {2019},
}

@article{9580,
  abstract     = {An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H into r parts and the size of the cut is the number of edges which have a vertex in each part. A classical result of Edwards says that every m-edge graph has a 2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts which exceed the expected size of a random cut by some multiple of the standard deviation. We study analogues of this and related results in hypergraphs. First, we observe that similarly to graphs, every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover, in the case where k = 3 and r = 2 this bound is best possible and is attained by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥ 4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant difference in behaviour, since the amount by which the size of the largest cut exceeds the expected size of a random cut is now considerably larger than the standard deviation.},
  author       = {Conlon, David and Fox, Jacob and Kwan, Matthew Alan and Sudakov, Benny},
  issn         = {1565-8511},
  journal      = {Israel Journal of Mathematics},
  number       = {1},
  pages        = {67--111},
  publisher    = {Springer},
  title        = {{Hypergraph cuts above the average}},
  doi          = {10.1007/s11856-019-1897-z},
  volume       = {233},
  year         = {2019},
}

@article{9585,
  abstract     = {An n-vertex graph is called C-Ramsey if it has no clique or independent set of size C log n. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have the same numbers of vertices and edges. Improving on earlier results of Alon, Balogh, Kostochka and Samotij, in this paper we prove this conjecture.},
  author       = {Kwan, Matthew Alan and Sudakov, Benny},
  issn         = {1088-6850},
  journal      = {Transactions of the American Mathematical Society},
  number       = {8},
  pages        = {5571--5594},
  publisher    = {American Mathematical Society},
  title        = {{Proof of a conjecture on induced subgraphs of Ramsey graphs}},
  doi          = {10.1090/tran/7729},
  volume       = {372},
  year         = {2019},
}

@article{9586,
  abstract     = {Consider integers  𝑘,ℓ  such that  0⩽ℓ⩽(𝑘2) . Given a large graph  𝐺 , what is the fraction of  𝑘 -vertex subsets of  𝐺  which span exactly  ℓ  edges? When  𝐺  is empty or complete, and  ℓ  is zero or  (𝑘2) , this fraction can be exactly 1. On the other hand, if  ℓ  is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.
Let  ℓ∗=min{ℓ,(𝑘2)−ℓ} . Our main result is that for any  𝑘  and  ℓ , the fraction of  𝑘 -vertex subsets that span  ℓ  edges is at most  log𝑂(1)(ℓ∗/𝑘)√ 𝑘/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.
Our proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube.},
  author       = {Kwan, Matthew Alan and Sudakov, Benny and Tran, Tuan},
  issn         = {1469-7750},
  journal      = {Journal of the London Mathematical Society},
  number       = {3},
  pages        = {757--777},
  publisher    = {Wiley},
  title        = {{Anticoncentration for subgraph statistics}},
  doi          = {10.1112/jlms.12192},
  volume       = {99},
  year         = {2019},
}

@article{9677,
  abstract     = {Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.},
  author       = {Kapil, Venkat and Rossi, Mariana and Marsalek, Ondrej and Petraglia, Riccardo and Litman, Yair and Spura, Thomas and Cheng, Bingqing and Cuzzocrea, Alice and Meißner, Robert H. and Wilkins, David M. and Helfrecht, Benjamin A. and Juda, Przemysław and Bienvenue, Sébastien P. and Fang, Wei and Kessler, Jan and Poltavsky, Igor and Vandenbrande, Steven and Wieme, Jelle and Corminboeuf, Clemence and Kühne, Thomas D. and Manolopoulos, David E. and Markland, Thomas E. and Richardson, Jeremy O. and Tkatchenko, Alexandre and Tribello, Gareth A. and Van Speybroeck, Veronique and Ceriotti, Michele},
  issn         = {0010-4655},
  journal      = {Computer Physics Communications},
  pages        = {214--223},
  publisher    = {Elsevier},
  title        = {{i-PI 2.0: A universal force engine for advanced molecular simulations}},
  doi          = {10.1016/j.cpc.2018.09.020},
  volume       = {236},
  year         = {2019},
}

@article{9680,
  abstract     = {Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen set of collective variables can significantly accelerate the exploration of phase space, albeit at the price of distorting the distribution of microstates. Efficient reweighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as metadynamics, variationally enhanced sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium manner under a time-dependent bias. We introduce an iterative unbiasing scheme that makes efficient use of all the trajectory data and that does not require the distribution to be evaluated on a grid. The method can thus be used even when the bias has a high dimensionality. We benchmark this approach against some of the existing schemes on model systems with different complexity and dimensionality.},
  author       = {Giberti, F. and Cheng, Bingqing and Tribello, G. A. and Ceriotti, M.},
  issn         = {1549-9626},
  journal      = {Journal of Chemical Theory and Computation},
  number       = {1},
  pages        = {100--107},
  publisher    = {American Chemical Society},
  title        = {{Iterative unbiasing of quasi-equilibrium sampling}},
  doi          = {10.1021/acs.jctc.9b00907},
  volume       = {16},
  year         = {2019},
}

@article{9689,
  abstract     = {A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water.},
  author       = {Cheng, Bingqing and Engel, Edgar A. and Behler, Jörg and Dellago, Christoph and Ceriotti, Michele},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  number       = {4},
  pages        = {1110--1115},
  publisher    = {National Academy of Sciences},
  title        = {{Ab initio thermodynamics of liquid and solid water}},
  doi          = {10.1073/pnas.1815117116},
  volume       = {116},
  year         = {2019},
}

@misc{9726,
  abstract     = {A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)},
  author       = {Ucar, Mehmet C and Lipowsky, Reinhard},
  publisher    = {American Chemical Society },
  title        = {{Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding}},
  doi          = {10.1021/acs.nanolett.9b04445.s001},
  year         = {2019},
}

@misc{9731,
  abstract     = {OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb)},
  author       = {Sigalova, Olga and Chaplin, Andrei and Bochkareva, Olga and Shelyakin, Pavel and Filaretov, Vsevolod and Akkuratov, Evgeny and Burskaia, Valentina and Gelfand, Mikhail S.},
  publisher    = {Springer Nature},
  title        = {{Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}},
  doi          = {10.6084/m9.figshare.9808772.v1},
  year         = {2019},
}

@misc{9783,
  abstract     = {Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb)},
  author       = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.},
  publisher    = {Springer Nature},
  title        = {{Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}},
  doi          = {10.6084/m9.figshare.9808760.v1},
  year         = {2019},
}

@misc{9784,
  abstract     = {Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.},
  author       = {Antoniou, Michael N. and Nicolas, Armel and Mesnage, Robin and Biserni, Martina and Rao, Francesco V. and Martin, Cristina Vazquez},
  publisher    = {Springer Nature},
  title        = {{MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells}},
  doi          = {10.6084/m9.figshare.9411761.v1},
  year         = {2019},
}

@misc{9786,
  author       = {Ruess, Jakob and Pleska, Maros and Guet, Calin C and Tkačik, Gašper},
  publisher    = {Public Library of Science},
  title        = {{Supporting text and results}},
  doi          = {10.1371/journal.pcbi.1007168.s001},
  year         = {2019},
}

@misc{9789,
  author       = {Pokusaeva, Victoria and Usmanova, Dinara R. and Putintseva, Ekaterina V. and Espinar, Lorena and Sarkisyan, Karen and Mishin, Alexander S. and Bogatyreva, Natalya S. and Ivankov, Dmitry and Akopyan, Arseniy and Avvakumov, Sergey and Povolotskaya, Inna S. and Filion, Guillaume J. and Carey, Lucas B. and Kondrashov, Fyodor},
  publisher    = {Public Library of Science},
  title        = {{Multiple alignment of His3 orthologues}},
  doi          = {10.1371/journal.pgen.1008079.s010},
  year         = {2019},
}

@misc{9790,
  author       = {Pokusaeva, Victoria and Usmanova, Dinara R. and Putintseva, Ekaterina V. and Espinar, Lorena and Sarkisyan, Karen and Mishin, Alexander S. and Bogatyreva, Natalya S. and Ivankov, Dmitry and Akopyan, Arseniy and Avvakumov, Sergey and Povolotskaya, Inna S. and Filion, Guillaume J. and Carey, Lucas B. and Kondrashov, Fyodor},
  publisher    = {Public Library of Science},
  title        = {{A statistical summary of segment libraries and sequencing results}},
  doi          = {10.1371/journal.pgen.1008079.s011},
  year         = {2019},
}