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Structural defects in 2D-transition metal dichalcogenides are critical in modulating their optical and electrical behavior. Nevertheless, precise defect control within the monolayer regime poses a significant challenge. Herein, a…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…
Pre-trained diffusion models have emerged as powerful generative priors for both unconditional and conditional sample generation, yet their outputs often deviate from the characteristics of user-specific target data. Such mismatches are…
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…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Differences in transcriptional regulatory networks underlie much of the phenotypic variation observed across organisms. Changes to cis-regulatory elements are widely believed to be the predominant means by which regulatory networks evolve,…
Although deep learning has produced dazzling successes for applications of image, speech, and video processing in the past few years, most trainings are with suboptimal hyper-parameters, requiring unnecessarily long training times. Setting…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
Parameter-efficient fine-tuning approaches have recently garnered a lot of attention. Having considerably lower number of trainable weights, these methods can bring about scalability and computational effectiveness. In this paper, we look…
The deformation of cellular membranes regulates trafficking processes, such as exocytosis and endocytosis. Classically, the Helfrich continuum model is used to characterize the forces and mechanical parameters that cells tune to accomplish…
Artificial neural networks are trained by a standard backpropagation learning algorithm with regularization to model and predict the systematics of -decay of heavy and superheavy nuclei. This approach to regression is implemented in two…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…
Multimodal learning has shown great potentials in numerous scenes and attracts increasing interest recently. However, it often encounters the problem of missing modality data and thus suffers severe performance degradation in practice. To…
Cell phenotype dynamic homeostasis contrasts with the inherent randomness of intracellular reactions. Although feedback control of master regulatory genes (MRG) is a key strategy for maintaining gene network expression ranges limited,…
The impact of shear deformation in $(1\,0\,1)[1\,0\,\bar{1}]$ system of non-modulated (NM) martensite in Ni$_2$MnGa ferromagnetic shape memory alloy is investigated by means of ab initio atomistic simulations. The shear system is associated…
Sequential fine-tuning of pretrained language encoders often overwrites previously acquired capabilities, but the forgetting behavior of parameter-efficient updates remains under-characterized. We present a controlled empirical study of…
Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous…
Deep learning has revolutionized medical and biological imaging, particularly in segmentation tasks. However, segmenting biological cells remains challenging due to the high variability and complexity of cell shapes. Addressing this…