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Jeongbin Park

Publications and source records attributed to Jeongbin Park.

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Mat-Pref: Verifiable-Reward Training Improves Compositional Reasoning in Inorganic Materials

Reinforcement learning from verifiable rewards (RLVR) has driven rapid progress in mathematical and code reasoning, but when extended to science, existing benchmarks do not decompose what generalizes: do gains reflect structural transfer, property transfer, or memorization? We introduce Mat-Pref, a benchmark of 10,837 ionic-substitution questions across 11 inorganic structure families, grounded in density functional theory calculations from the Materials Project, with three evaluation splits that isolate in-distribution performance, generalization to entirely held-out structure families, and cross-property transfer: applying band-gap reasoning to hosts seen during training only through formation-energy supervision. Four zero-shot frontier models (70-671B parameters) remain in the 33-54% range on every split, confirming that scale alone does not resolve the compositional chemical reasoning this task demands. A two-stage pipeline of supervised fine-tuning followed by Group Relative Policy Optimization (GRPO) lifts Qwen3-8B to 65.2% in-distribution and 71.6% on held-out families, exceeding zero-shot Qwen3-235B by over 20 percentage points on both structural-generalization splits. Self-consistency sampling shows that the SFT policy can already produce correct answers but cannot reliably surface them as the modal response; GRPO reshapes the distribution so that correct answers become modal rather than merely reachable, and this sharper commitment is visible mechanistically: logit lens analysis reveals a ${\sim}$20pp advantage in answer crystallization at the critical decision layer. We formalize this observation as a distractor-permutation consistency metric under which GRPO narrows the gap between lenient scoring (at least one permutation correct) and strict scoring (all permutations correct) from 24.0 to 14.3 percentage points.

cs.LG

Site4Drug: Predicting Drug-Binding Target Sites with an AI Agent

Selecting where to intervene on a protein (i.e., choosing a targetable site) is often a more ambiguous and failure-prone bottleneck than selecting what binds, especially for membrane proteins where accessibility, topology, and post-translational modifications (PTMs) constrain actionable regions. We present Site4Drug, a modality-aware site-finding agent that outputs a ranked list of targetable regions with explicit constraints, evidence summaries, risk flags, and a traceable decision log. Rather than requiring users to specify the drug modality upfront, Site4Drug can recommend a binding modality (e.g., antibody/peptide-like vs small-molecule) from the same evidence used for site discovery, including topology, hydropathy, PTM propensity, disulfides, domain context, and sequence. Importantly, this evidence is applied consistently across modalities, including small-molecule pocket discovery, to avoid selecting chemically plausible but biologically occluded sites.

q-bio.BM

CFD-based design optimization of a 5 kW ducted hydrokinetic turbine with practical constraints

Ducted hydrokinetic turbines enhance energy-harvesting efficiency by better conditioning the flow to the blades, which may yield higher power output than conventional freestream turbines for the same reference area. In this work, we present a ducted hydrokinetic turbine design obtained by simultaneously optimizing the duct, blade, and hub geometries. Our optimization framework combines a CFD solver, an adjoint solver, and a gradient-based optimizer to efficiently explore a large design space, together with a feature-based parameterization method to handle the complex geometry. Practical geometrical constraints ensure the manufacturability of the duct in terms of a minimum thickness and the housing of a 5 kW generator within the hub. The optimization converges to a short, thin duct with a rounded leading edge and an elongated hub protruding the duct inlet. The optimized ducted turbine achieves up to 50% efficiency when evaluated by RANS/URANS solvers despite a bulky hub, outperforming the 45% efficiency of the freestream Bahaj turbine featuring the same hub. This work showcases the effectiveness of CFD-based optimization in advancing ducted turbine designs and demonstrates the hydrodynamic benefits of a ducted configuration, paving the way for future research and real-world applications.

physics.flu-dyn

Metrics on permutations with the same peak set

Let $S_n$ be the symmetric group on the set $\{1,2,\ldots,n\}$. Given a permutation $σ=σ_1σ_2 \cdots σ_n \in S_n$, we say it has a peak at index $i$ if $σ_{i-1}<σ_i>σ_{i+1}$. Let $\text{Peak}(σ)$ be the set of all peaks of $σ$ and define $P(S;n)=\{σ\in S_n\, | \,\text{Peak}(σ)=S\}$. In this paper we study the Hamming metric, $\ell_\infty$-metric, and Kendall-Tau metric on the sets $P(S;n)$ for all possible $S$, and determine the minimum and maximum possible values that these metrics can attain in these subsets of $S_n$.

math.CO

CFD-based Design Optimization of Ducted Hydrokinetic Turbines

Hydrokinetic turbines extract kinetic energy from moving water to generate renewable electricity, thus contributing to sustainable energy production and reducing reliance on fossil fuels. It has been hypothesized that a duct can accelerate and condition the fluid flow passing the turbine blades, improving the overall energy extraction efficiency. However, no substantial evidence has been provided so far for hydrokinetic turbines. To investigate this problem, we perform a CFD-based optimization study with a blade-resolved Reynolds-averaged Navier--Stokes (RANS) solver to explore the design of a ducted hydrokinetic turbine that maximizes the efficiency of energy extraction. To handle the high-dimensional design space of the blade and duct geometry, we use a gradient-based optimization approach where the gradients are computed using the adjoint method. The final design is re-evaluated through higher-fidelity unsteady RANS (URANS) simulations. Our optimized ducted turbine achieves an efficiency of about 54% over a range of operating conditions, higher than the typical 46% efficiency of unducted turbines such as the well-known Bahaj model.

physics.flu-dyn