Quantitative Biology
The brain is composed of billions of neurons with virtually endless morphologies and ion channel compositions, resulting in unique extracellular waveforms. Nevertheless, almost all neuronal morphologies can be reduced to a simple…
Recent advancements in single-cell multi-omics, particularly RNA-seq, have provided profound insights into cellular heterogeneity and gene regulation. While pre-trained language model (PLM) paradigm based single-cell foundation models have…
Tokenization sits at the boundary between high-throughput genomic input and GPU compute, posing challenges in both algorithm design and system throughput. Overlapping k-mer tokenization can introduce information leakage under masked…
In the brain, neural activity undergoes directed flows between states, thus breaking time-reversal symmetry. At the same time, animals also exhibit irreversible flows between behavioral states. Yet it remains unclear whether -- and how --…
This article proposes a research and development direction that would lead to the creation of next-generation intelligent technical systems. A distinctive feature of these systems is their ability to undergo evolutionary change. Cognitive…
In this study, we introduce a sensitivity analysis methodology for stochastic systems in chemistry, where dynamics are often governed by random processes. Our approach is based on gradient estimation via finite differences, averaging…
Multilevel selection occurs when short-term individual-level reproductive interests conflict with longer-term group-level fitness effects. Detecting and quantifying this phenomenon is key to understanding evolution of traits ranging from…
Living cells maintain size homeostasis by actively compensating for size fluctuations. Here, we present two stochastic maps that unify phenomenological models by integrating fluctuating single-cell growth rates and size-dependent noise…
Synchronized rhythmic oscillatory activity in the beta frequency band in the basal ganglia (BG) is a hallmark of Parkinson's disease (PD). Recent experiments and theoretical studies have demonstrated the crucial roles of T-type and L-type…
A highly diluted aqueous solution of histamine was studied by molecular dynamics using the TIP3P and SPC/E water models. It was shown that the local structure of the solution around histamine is determined by local Coulomb interactions and…
Examination of T-cell receptor (TCR) clonality has become a way of understanding immunologic response to cancer and its interventions in recent years. An aspect of these analyses is determining which receptors expand or contract…
Psychedelics have shown potential in treating a range of mental health conditions, yet far less is known about their impact on creativity. This study examined three components of creativity-divergent thinking, cognitive reflection, and…
Cellular decision-making under stress involves rapid pathway selection despite energy scarcity. Here we demonstrate that thermodynamic constraints actively drive energy-efficient sporulation, where continuous metabolic sources enable system…
We explore the connection between evolution and large-deviation theory. To do so, we study evolutionary dynamics in which individuals experience mutations, reproduction, and selection using variants of the Moran model. We show that, in the…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Microplate-based 'omic studies of large clinical cohorts can massively accelerate biomedical research, but experimental power and veracity may be negatively impacted when plate positional effects confound clinical variables of interest.…
Background. Knee Osteoarthritis (OA) is a common chronic joint condition, and its prevalence increases with age. This study aims to examine whether flattened vertical ground reaction force (vGRF) waveforms and reduced knee range of motion…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
Efficient navigation in swarms often relies on the emergence of decentralized approaches that minimize traversal time or energy. Stigmergy, where agents modify a shared environment that then modifies their behavior, is a classic mechanism…
A hallmark of aging is loss of information in gene regulatory networks. These networks are tightly connected, raising the question of whether information could be restored by perturbing single genes. We develop a simple theoretical…