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Goal-oriented de novo molecule design, namely generating molecules with specific property or substructure constraints, is a crucial yet challenging task in drug discovery. Existing methods, such as Bayesian optimization and reinforcement…
The Unified Modeling Language (UML) is commonly used in introductory Computer Science to teach basic object-oriented design. However, there appears to be a lack of suitable software to support this task. Many of the available programs that…
A Python package for post-processing of plane two-dimensional data from computational fluid dynamics simulations is presented. The package, called turbulucid, provides means for scripted, reproducible analysis of large simulation campaigns…
Physiologically Based Pharmacokinetic (PBPK) modeling is a cornerstone of model-informed drug development (MIDD), providing a mechanistic framework to predict drug absorption, distribution, metabolism, and excretion (ADME). Despite its…
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful…
Vision In-Context Learning (VICL) enables inpainting models to quickly adapt to new visual tasks from only a few prompts. However, existing methods suffer from two key issues: (1) selecting only the most similar prompt discards…
This paper presents the design and implementation of a modular multi-document interface (MDI) framework for scientific visualization and simulation in the Java Virtual Machine (JVM) ecosystem. The framework emphasizes architectural…
MiMiC is a flexible and efficient framework for multiscale simulations in which different subsystems are treated by individual client programs. In this work, we present a new interface with OpenMM to be used as an MM client program and we…
PQuantML is a new open-source, hardware-aware neural network model compression library tailored to end-to-end workflows. Motivated by the need to deploy performant models to environments with strict latency constraints, PQuantML simplifies…
CLPGUI is a graphical user interface for visualizing and interacting with constraint logic programs over finite domains. In CLPGUI, the user can control the execution of a CLP program through several views of constraints, of finite domain…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our…
DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
The integration of deep learning, particularly AI-Generated Content, with high-quality data derived from ab initio calculations has emerged as a promising avenue for transforming the landscape of scientific research. However, the challenge…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…
This paper introduces QuanUML, an extension of the Unified Modeling Language (UML) tailored for quantum software systems. QuanUML integrates quantum-specific constructs, such as qubits and quantum gates, into the UML framework, enabling the…
Human expertise in chemistry and biomedicine relies on contextual molecular understanding, a capability that large language models (LLMs) can extend through fine-grained alignment between molecular structures and text. Recent multimodal…
Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…