Publications by authors named "Ayoti Patra"

3 Publications

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Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.

Hum Mutat 2019 09 23;40(9):1280-1291. Epub 2019 Jun 23.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland.

The integrative analysis of high-throughput reporter assays, machine learning, and profiles of epigenomic chromatin state in a broad array of cells and tissues has the potential to significantly improve our understanding of noncoding regulatory element function and its contribution to human disease. Here, we report results from the CAGI 5 regulation saturation challenge where participants were asked to predict the impact of nucleotide substitution at every base pair within five disease-associated human enhancers and nine disease-associated promoters. A library of mutations covering all bases was generated by saturation mutagenesis and altered activity was assessed in a massively parallel reporter assay (MPRA) in relevant cell lines. Reporter expression was measured relative to plasmid DNA to determine the impact of variants. The challenge was to predict the functional effects of variants on reporter expression. Comparative analysis of the full range of submitted prediction results identifies the most successful models of transcription factor binding sites, machine learning algorithms, and ways to choose among or incorporate diverse datatypes and cell-types for training computational models. These results have the potential to improve the design of future studies on more diverse sets of regulatory elements and aid the interpretation of disease-associated genetic variation.
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http://dx.doi.org/10.1002/humu.23797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879779PMC
September 2019

Fast forward to the classical adiabatic invariant.

Phys Rev E 2017 Mar 10;95(3-1):032122. Epub 2017 Mar 10.

Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.

We show how the classical action, an adiabatic invariant, can be preserved under nonadiabatic conditions. Specifically, for a time-dependent Hamiltonian H=p^{2}/2m+U(q,t) in one degree of freedom, and for an arbitrary choice of action I_{0}, we construct a so-called fast-forward potential energy function V_{FF}(q,t) that, when added to H, guides all trajectories with initial action I_{0} to end with the same value of action. We use this result to construct a local dynamical invariant J(q,p,t) whose value remains constant along these trajectories. We illustrate our results with numerical simulations. Finally, we sketch how our classical results may be used to design approximate quantum shortcuts to adiabaticity.
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http://dx.doi.org/10.1103/PhysRevE.95.032122DOI Listing
March 2017

Classical and Quantum Shortcuts to Adiabaticity in a Tilted Piston.

J Phys Chem B 2017 04 12;121(15):3403-3411. Epub 2016 Oct 12.

Department of Physics, University of Maryland , College Park, Maryland 20742, United States.

Adiabatic quantum state evolution can be accelerated through a variety of shortcuts to adiabaticity. In one approach, a counterdiabatic quantum Hamiltonian, Ĥ, is constructed to suppress nonadiabatic excitations. In the analogous classical problem, a counterdiabatic classical Hamiltonian, H, ensures that the classical action remains constant even under rapid driving. Both the quantum and classical versions of this problem have been solved for the special case of scale-invariant driving, characterized by linear expansions, contractions, or translations of the system. Here we investigate an example of a non-scale-invariant system, a tilted piston. We solve exactly for the classical counterdiabatic Hamiltonian, H(q, p, t), which we then quantize to obtain a Hermitian operator, Ĥ(t). Using numerical simulations, we find that Ĥ effectively suppresses nonadiabatic excitations under rapid driving. These results offer a proof of principle, beyond the special case of scale-invariant driving, that quantum shortcuts to adiabaticity can successfully be constructed from their classical counterparts.
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http://dx.doi.org/10.1021/acs.jpcb.6b08769DOI Listing
April 2017