Quantitative Biology
Understanding cellular machinery requires atomic-scale reconstruction of large biomolecular assemblies. However, predicting the structures of these systems has been constrained by hardware memory requirements of models like AlphaFold 3,…
Autonomous LLM agents require structured long-term memory, yet current "append-and-evolve" systems like A-MEM face O(N^2) write-latency and excessive token costs. We introduce D-MEM (Dopamine-Gated Agentic Memory), a biologically inspired…
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) and Acinetobacter baumannii (CRAB) represent a major clinical and epidemiological challenge and pose a growing threat to public health and the environment. Accordingly, CRPA and CRAB were…
Modern neuroscience has accumulated extensive evidence on perception, memory, prediction, valuation, and consciousness, yet still lacks an explicit operational architecture capable of integrating these phenomena within a unified…
Intracranial language brain-computer interfaces (BCIs) are a promising route for restoring communication in people with severe motor and speech impairments, but clinical translation remains limited by fragmented evidence and unresolved…
Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identification of RBPs is complicated by their extreme sequence…
From 1/f noise to neuronal avalanches, evidence of scaling in brain activity has been increasingly linked to tuning to or near criticality. The concept of scaling is intimately related to the renormalization group (RG), in essence providing…
Schemas -- abstract relational structures that capture the commonalities across experiences -- are thought to underlie humans' and animals' ability to rapidly generalize knowledge, rebind new experiences to existing structures, and flexibly…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
Background: The surge in single-cell omics data exposes limitations in traditional, manually defined analysis workflows. AI agents offer a paradigm shift, enabling adaptive planning, executable code generation, traceable decisions, and…
Neurons communicate with downstream systems via sparse and incredibly brief electrical pulses, or spikes. Using these events, they control various targets such as neuromuscular units, neurosecretory systems, and other neurons in connected…
Traditional artificial neural networks consist of nodes with non-oscillatory dynamics. Biological neural networks, on the other hand, consist of oscillatory components embedded in an oscillatory environment. Motivated by this feature of…
The cognitive state of mind concerning a range of choices to be made can effectively be modelled in terms of an element of a high-dimensional Hilbert space. The dynamics of the state of mind resulting form information acquisition is…
Morphogenesis is the biological process that causes the emergence and changes of patterns (tissues and organs) in living organisms. It is a robust, self-organising mechanism, governed by Genetic Regulatory Networks (GRN), that hasn't been…
We show how biological grouping-particularly species formation-can emerge from interactions among populations governed by number-theoretic structure. In our framework, a species is identified with a $p$-Sylow subgroup of a community…
This study presents the development of the PsyCogMetrics AI Lab (psycogmetrics.ai), an integrated, cloud-based platform that operationalizes psychometric and cognitive-science methodologies for Large Language Model (LLM) evaluation. Framed…
The synchronized activity of neuronal populations can lead to pathological over-synchronization in conditions such as epilepsy and Parkinson disease. Such states can be desynchronized by brief electrical pulses. But when the underlying…
Speech production and perception are the main ways humans communicate daily. Prior brain-to-text decoding studies have largely focused on a single modality and alphabetic languages. Here, we present a unified brain-to-sentence decoding…
Cryo-electron microscopy (cryo-EM) has emerged as a powerful technique for determining the three-dimensional structures of biological molecules at near-atomic resolution. However, reconstructing helical assemblies presents unique challenges…
Parkinson's disease (PD) is projected to increase substantially due to population aging, making early diagnosis increasingly important, as timely detection may delay progression and reduce long-term complications. Retinal microvasculature…