arXiv subjects

Po-Ta Chen

Publications and source records attributed to Po-Ta Chen.

2 recordsLinked to original sources

arXiv2023

Gene activity fully predicts transcriptional bursting dynamics

Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct real-time measurements of endogenous transcriptional bursting with single-mRNA sensitivity. Leveraging the diverse transcriptional activities in early fly embryos, we uncover stringent relationships between bursting parameters. Specifically, we find that the durations of ON and OFF periods are linked. Regardless of the developmental stage or body-axis position, gene activity levels predict individual alleles' average ON and OFF periods. Lowly transcribing alleles predominantly modulate OFF periods (burst frequency), while highly transcribing alleles primarily tune ON periods (burst size). These relationships persist even under perturbations of cis-regulatory elements or trans-factors and account for bursting dynamics measured in other species. Our results suggest a novel mechanistic constraint governing bursting dynamics rather than a modular control of distinct parameters by distinct regulatory processes.

q-bio.MN↗

arXiv2012

Restoration of the Derivative Discontinuity in Kohn-Sham Density Functional Theory: An Efficient Scheme for Energy Gap Correction

From the perspective of perturbation theory, we propose a systematic procedure for the evaluation of the derivative discontinuity (DD) of the exchange-correlation energy functional in Kohn-Sham density functional theory (KS-DFT), wherein the exact DD can in principle be obtained by summing up all the perturbation corrections to infinite order. Truncation of the perturbation series at low order yields an efficient scheme for obtaining the approximate DD. While the zeroth-order theory yields a vanishing DD, the first-order correction to the DD can be expressed as an explicit universal functional of the ground-state density and the KS lowest unoccupied molecular orbital density, allowing the direct evaluation of the DD in the standard KS method without extra computational cost. The fundamental gap can be predicted by adding the estimated DD to the KS gap. This scheme is shown to be accurate in the prediction of the fundamental gaps for a wide variety of atoms and molecules.

physics.chem-ph↗