Research
Research
Research
Research
5,835+ open-access research outputs.
We report the largest trapped-ion hardware demonstration of lattice protein-folding optimization to date, using bias-field digitized counterdiabatic quantum optimization (BF-DCQO) on a fully connected…
Offline preference optimization methods, such as Direct Preference Optimization (DPO), offer significant advantages in aligning Large Language Models (LLMs) with human values. However, achieving optim…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open …
The inverse Potts problem for estimating evolutionary single-site fields and pairwise couplings in homologous protein sequences from their single-site and pairwise amino acid frequencies observed in t…
We formulate and analyse an optimal control problem for the coagulation-fragmentation equation, where a scalar, time-dependent control modulates the coagulation rate by multiplying the coagulation ker…
Predicting the functional impact of single amino acid substitutions (SAVs) is central to understanding genetic disease and engineering therapeutic proteins. While protein language models and structure…
Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, there is…
Pluto possesses a thin atmosphere primarily composed of N2, with minor constituents including CO and CH4. Photochemical processes generate distinct haze layers as observed by the New Horizons spacecra…
The identification of reliable molecular biomarkers for Parkinson's disease remains challenging due to its multifactorial nature. Although protein sequences constitute a fundamental and widely availab…
Colloid models have frequently been used to successfully describe the influence of protein-protein interactions on antibody solution properties, but they suffer from inherent problems due to the aniso…
Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the …
We study nonlinear constrained optimization problems in which only function evaluations of the objective and constraints are available. Existing zeroth-order methods rely on noisy gradient and Jacobia…
The terahertz (THz) spectral regime offers unique opportunities for next-generation biochemical sensing due to its non-destructive, label-free probing capability and strong sensitivity to molecular vi…
Agentic vision-language models increasingly act through extended interactions, but most evaluations still focus on single-image, single-turn correctness. We introduce AMIGO (Agentic Multi-Image Ground…
Chiral phonons are mirror-symmetric vibrations that correspond to twisting and rotational motions of atoms. In chiral biomolecules, they correspond to low-energy terahertz (THz)-range vibrations of th…
Building blocks of life such as amino acids, nucleobases, and fatty acids are central to prebiotic chemistry and represent key targets in the search for planetary biosignatures. In planetary materials…
The rapid scaling of Protein Language Models (PLMs) has unlocked unprecedented accuracy in protein structure prediction and design, but the quadratic memory growth of the Key-Value (KV) cache during i…
We introduce the Free-Market Algorithm (FMA), a novel metaheuristic inspired by free-market economics. Unlike Genetic Algorithms, Particle Swarm Optimization, and Simulated Annealing -- which require …
Landing methods have recently emerged in Riemannian matrix optimization as efficient schemes for handling nonlinear equality constraints without resorting to costly retractions. These methods decompos…
Recent advances in general-purpose foundation models have stimulated the development of large biological sequence models. While natural language shows symbolic granularity (characters, words, sentence…
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