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AI & Data Science Preprint PDF DOI

ObjectGraph: From Document Injection to Knowledge Traversal -- A Native File Format for the Agentic Era

Mohit Dubey, Open Gigantic · 2026

Every document format in existence was designed for a human reader moving linearly through text. Autonomous LLM agents do not read - they retrieve. This fundamental mismatch forces agents to inject en…

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Engineering Preprint PDF DOI

On the Nesterov's acceleration: A NAIM perspective

Rachit Mehra, M Parimi, Amol Yerudkar, S.R. Wagh, Navdeep Singh · 2026

We present a unifying Nearly Asymptotically Invariant Manifold (NAIM) framework for understanding Nesterovs Accelerated Gradient (NAG) method. By lifting the first-order gradient flow into a second-or…

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Physics Preprint PDF DOI

Molecular Dynamics simulations of Al-Ti metallic alloy melts using a transferable machine-learning potential

Yuna Kato, Jurgen Brillo, Dirk Holland-Moritz, Fan Yang, Thomas C. Hansen, Thomas Voigtmann, Linnea Heitmeier · 2026

We investigate the structural and dynamical properties of binary aluminum-titanium liquid metallic alloys, as a function of temperature and composition. We make use of MD-simulations, using a transfer…

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Chemistry Preprint PDF DOI

Solv-eze: Automated Placement of Explicit Water Molecules Using 3D-RISM

Felipe Silva Carvalho, Steven Ramsey, Tom Kurtzman, Tyler Luchko · 2026

Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protoco…

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Chemistry Preprint PDF DOI

Excitation of Low-Frequency Modes and the Effects of Protein Dynamics on Spectral Densities of Bacteriochlorophyll Molecules

Sayan Maity, Tristan A. Mauck, Ulrich Kleinekathofer · 2026

In the theory of open quantum systems, spectral densities are key quantities for modeling the dynamics and spectroscopic properties of the system under investigation. In the case of light-harvesting c…

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Physics Preprint PDF DOI

Improved Electrochemical Performance and Diffusion kinetics by Boron-doping in Na$_{0.66}$Mn$_{0.8}$Fe$_{0.2}$O$_{2}$ Layered Cathodes for Sodium-Ion Batteries

Jayashree Pati, P. Senthilkumar, Deepak Seth, Riya Gulati, Manish Kr. Singh, Madhav Sharma, Anita Dhaka, M. Ali Haider, Rajendra S. Dhaka · 2026

We report the electrochemical investigation and study the diffusion kinetics of boron doped Na$_{0.66}$Mn$_{0.8}$Fe$_{0.2}$O$_{2}$ (B-NMFO) cathode materials for sodium-ion batteries. Notably, the B-N…

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Physics Preprint PDF DOI

Trillion-atom molecular dynamics simulations with ab initio accuracy

Pengfei Suo, Wudi Cao, Xingxing Wu, Wenjie Zhang, Zheyong Fan, Shuanghan Xian, Rui Wang, Cheng Qian, Chao Liang, Qinghong Yuan, Xiaoshuang Chen, Pengfei Guan, Jingde Bu, Hongzhen Tian, Yanjing Su, Feng Ding, Lin-Wang Wang · 2026

Material properties are fundamentally dictated by multiscale phenomena, which often reach mesoscale in size. The {\mu}m mesoscale is also the size which can be observed directly under an optical micro…

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Physics Preprint PDF DOI

Synchronized molecular dynamics method for thin-layer flows of complex fluids

Shugo Yasuda, Kotaro Oda, Fumito Muragaki, Yuta Taketa, Masashi Iwayama, Tomohide Ina · 2026

We propose a multiscale computational method for thin-layer flows of complex fluids, termed the synchronized molecular dynamics (SMD) method, which directly couples local molecular dynamics (MD) simul…

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AI & Data Science Preprint PDF DOI

From Skill Text to Skill Structure: The Scheduling-Structural-Logical Representation for Agent Skills

Qiliang Liang, Hansi Wang, Zhong Liang, Yang Liu · 2026

LLM agents increasingly rely on reusable skills, capability packages that combine instructions, control flow, constraints, and tool calls. In most current agent systems, however, skills are still repr…

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AI & Data Science Preprint PDF DOI

MAEO: Multiobjective Animorphic Ensemble Optimization for Scalable Large-scale Engineering Applications

Omer F. Erdem, Dean Price, Paul Seurin, Majdi I. Radaideh · 2026

Multiobjective optimization remains challenging for many scientific and engineering problems due to the need to balance convergence, diversity, and computational efficiency across high-dimensional obj…

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Physics Preprint PDF DOI

The influence of implantation conditions on dopant activation in Al-implanted 4H-SiC: A MD study applying an Al potential fitted to DFT barriers

Sabine Leroch, Robert Stella, Andreas Hossinger, Lado Filipovic · 2026

We present molecular dynamics simulations of shallow Al implantation in 4H-SiC to clarify how implantation temperature and dose control defect evolution and dopant activation during early annealing. U…

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Computer Science Preprint PDF DOI

Agentic AI-assisted coding offers a unique opportunity to instill epistemic grounding during software development

Magnus Palmblad, Jared M. Ragland, Benjamin A. Neely · 2026

The capabilities of AI-assisted coding are progressing at breakneck speed. Chat-based vibe coding has evolved into fully fledged AI-assisted, agentic software development using agent scaffolds where t…

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Physics Preprint PDF DOI

Data-Driven Thermal and Mechanical Modeling of Defective Covalent Organic Frameworks

Aleksander Szewczyk, Leonardo Medrano Sandonas, David Bodesheim, Bohayra Mortazavi, Gianaurelio Cuniberti · 2026

Covalent Organic Frameworks (COFs) are versatile two-dimensional (2D) materials for flexible electronics, catalysis, and sensing, owing to their tunable architectures and large surface areas. However,…

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Physics Preprint PDF DOI

Enabling Biomolecular Simulations with Neural Network Potentials in GROMACS

Lukas Mullender, Berk Hess, Erik Lindahl · 2026

Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to…

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AI & Data Science Preprint PDF DOI

MD-Face: MoE-Enhanced Label-Free Disentangled Representation for Interactive Facial Attribute Editing

Xuan Cui, Yunfei Zhao, Bo Liu, Wei Duan, Xingrong Fan · 2026

GAN-based facial attribute editing is widely used in virtual avatars and social media but often suffers from attribute entanglement, where modifying one face attribute unintentionally alters others. W…

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Physics Preprint PDF DOI

Layer-mediated tuning of spin and valley physics in stacked tetragonal altermagnetic bilayers

Jianke Tian, Xiaowen Zhou, Gui-Bin Liu · 2026

As an emerging magnetic phase, altermagnets (AMs) with collinear compensated magnetism in real space and alternating spin splitting in the band structure have attracted widespread attention. Here, bas…

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Chemistry Preprint PDF DOI

Beyond the Virial Expansion: Microscopic Origins of Partial Molar Volumes in LiCl Solutions

Chun-Ting Lin, Diganta Dasgupta, Tinglu Yang, Cesare Malosso, Giulia Sormani, Colin Egan, Giovanni Bussi, Ali Hassanali, Paul S. Cremer · 2026

Although electrolyte density measurements have been reported for over a century, employing them to obtain accurate partial molar volume (PMV) profiles as a function of salt concentration has remained …

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AI & Data Science Preprint PDF DOI

Which Small-Sample Correction Should Be Used When Analyzing Stepped-Wedge Designs with Time-Varying Treatment Effects?

Yongdong Ouyang, Monica Taljaard, James P. Hughes, Fan Li · 2026

Stepped-wedge cluster randomized trials (SW-CRTs) evaluate interventions rolled out across clusters over time. Standard analyses typically use immediate-treatment (IT) models, which assume effects beg…

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Computer Science Preprint PDF DOI

Coordinatewise Balanced Covering for Linear Gain Graphs, with an Application to Coset-List Min-2-Lin over Powers of Two

Faruk Alpay, Levent Sarioglu · 2026

We study a list-constrained extension of modular equation deletion over powers of two, called Coset-List Min-2-Lin$^{\pm}$ over $\mathbb{Z}/2^d\mathbb{Z}$. Each variable is restricted to a dyadic cose…

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Biology & Life Sciences Preprint PDF DOI

MDAgent: A Multi-Agent Framework for End-to-End Molecular Dynamics Research

Zhenyu Ma, Chunyi Yang, Yuyang Song, Jingyi Zhu, Letian Yang, Limei Xu, Min Xiao, Xukai Jiang · 2026

Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structural changes, molecular recognition, transmembrane transport, and functional mechanisms. However, its practical bo…

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