arXiv subjects

Yi Isaac Yang

Publications and source records attributed to Yi Isaac Yang.

17 recordsLinked to original sources

arXiv2026

A Massively Scalable Ligand-Protein Dissociation Dynamic Database Derived from Atomistic Molecular Modelling

Understanding the kinetics of drug-protein interactions is paramount for drug design, yet the field lacks large-scale, dynamic data to move beyond static structural analysis. Here, we present DD-03B, a massively scalable database providing dynamic, all-atom dissociation trajectories for a broad set of ligand-protein complexes. Utilising and extending a validated computational pipeline, we generated dissociation trajectories for 19,037 ligand-protein complexes sourced from PDBbind+v2020R1, resulting in a repository of approximately 0.3 billion simulation frames totalling 40 TB in size. For these systems-which possess experimental binding affinities (kd) but typically lack measured koff rates-we computed and assigned dissociation rate constants through trajectory reweighting. Our analysis reveals that protein-ligand complexes can be categorised into three mechanistic types (pathway-dominant, open-pocket, and entropy-pocket systems), each requiring distinct strategies for accurate kinetic characterisation. Together with our previously released DD-13M, DD-03B forms the core of the expandable Dissociation Dynamic Database (DDD) project, which will be continuously augmented with new trajectories. This large-scale, publicly available resource establishes a critical foundation for training and benchmarking next-generation generative AI models to predict and optimise drug-protein dissociation kinetics.

physics.comp-ph↗

arXiv2026

Electronic Collective Variables for Chemical Reactions

Chemical reaction sampling critically depends on collective variables (CVs) that capture the slow degrees of freedom governing reactive transformations. However, existing reaction CVs are often defined in geometric space or learned in a system-specific manner, which limits their transferability and leaves open the more fundamental question of how reaction progress should be represented. From a physical perspective, chemical reactions are defined by electron redistribution. Here, we introduce a charge-space electronic collective variable that describes the electronic component of reaction progress in a common linear form based on atomic charges. To enable its use in enhanced sampling, atomic charges and the corresponding CV gradients are provided by a neural-network model trained on QM/MM data within an iterative sampling-training workflow. Across multiple reactions in aqueous and enzymatic environments, we show that this electronic CV can be constructed in a common charge-space form, with the corresponding coefficients assigned in a simple manner from charge differences between relevant states. Our simulations further show that reaction progress generally involves coupled electronic and conformational components, and that the same framework can also be extended to restrain side reactions. These findings support charge-based electronic CVs as a physically motivated framework for describing the electronic component of chemical reaction progress with reduced reliance on handcrafted geometric descriptors.

physics.chem-ph↗

arXiv2026

A Novel 4-D Dataset Paradigm for Studying Complete Ligand-Protein Dissociation Dynamics

The kinetics and dynamics of drug-protein binding and dissociation are crucial to understanding drug absorption and metabolism. Despite advances in artificial intelligence (AI) tools for drug-protein interaction studies, existing training datasets remain limited to static structures or quasi-static conformations. This paper proposes a novel computational approach for rapidly generating drug-protein dissociation trajectories and presents the inaugural dynamically time-resolved 4-D (t, x, y, z) trajectory database DD-13M. This dataset captures over 26,000 complete dissociation processes for 565 ligand-protein complexes, providing nearly 13 million frames of all-atom simulation trajectories. A deep equivariant generative model, UnbindingFlow, was trained using the DD-13M dataset. This model has the capacity to produce dissociation trajectories for novel targets whilst accurately predicting their rate constants (koff). DD-13M introduces a new type of training dataset for AI models, establishing a de novo paradigm for studying the dynamics of drug-protein interactions.

physics.comp-ph↗

arXiv2026

Great Restraining Wall in Multidimensional Collective Variable Space

Enhanced sampling methods are pivotal for exploring rare events in molecular dynamics (MD), yet face challenges in high-dimensional collective variable (CV) spaces where exhaustive sampling becomes computationally prohibitive. While techniques like metadynamics (MetaD) and path-CV enable targeted free energy surface (FES) reconstruction, they often struggle with confinement stability, hyperparameter sensitivity, and geometric flexibility. This work introduces the Great Restraining Wall (GW) method, a robust framework for efficient FES sampling within predefined CV subspaces, addressing these limitations through a novel kernel density estimation (KDE)-derived restraining potential. GW operates by constructing a bias potential that confines sampling to user defined regions ranging from multidimensional masks to 1D pathways via asymptotically half-harmonic barriers. Unlike MetaD variants requiring iterative bias deposition, GW potential is derived from a cumulative distribution function, ensuring confinement without manual hyperparameter tuning. GW provides a versatile, stable, and efficient framework for targeted FES sampling, particularly beneficial for complex biomolecular systems with intricate CV landscapes. Its integration with existing enhanced sampling protocols opens avenues for studying ligand binding, conformational transitions, and other rare events with unprecedented precision. Future work will explore GW extension to adaptive regions and machine learning-guided CV discovery.

physics.comp-ph↗

arXiv2025

Collective Variables Based on Multipole Expansion of Ewald Summation for Crystallization

Crystallization, a fundamental phase transition process governing material formation in natural and industrial contexts, involves the spontaneous emergence of long-range structural order from disordered phases. This long-range periodicity involves spatial and molecular orientation order. Molecular dynamics (MD) simulations of crystallization require collective variables (CVs) that accurately distinguish this long-\range periodicity. Existing CVs based on local descriptors (e.g., bond-orientational order) often lack transferability across crystal structures. To address this, we propose a unified CV framework derived from the multipole expansion of Ewald summation: a mathematical formalism bridging X-ray diffraction (XRD) principles and electrostatic energy computation in MD. By projecting atomic configurations onto a basis of spherical harmonics (complete for angular function representation), our CV achieves high-fidelity encoding of both translational and orientational order. Metadynamics simulations demonstrate that this CV drives efficient sampling of polymorphic pathways for known crystals and predicts stable phases even without crystal structures. This approach shows potential as a transferable platform for ab initio crystal structure prediction.

cond-mat.stat-mech↗

arXiv2025

Performing Path Integral Molecular Dynamics Using Artificial Intelligence Enhanced Molecular Simulation Framework

This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the framework effectively mitigates the computational complexity and resource-intensive limitations associated with conventional PIMD approaches. By integrating machine learning force fields (MLFFs) into the framework, we rigorously tested its performance through two representative cases: a small-molecule reaction system (double proton transfer in formic acid dimer) and a bulk-phase transition system (water-ice phase transformation). Computational results demonstrate that the proposed framework achieves accelerated PIMD simulations while preserving quantum mechanical accuracy. These findings show that nuclear quantum effects can be captured for complex molecular systems, using relatively low computational cost.

physics.chem-ph↗

arXiv2025

A Sinking Approach to Explore Arbitrary Areas in Free Energy Landscapes

To address the time-scale limitations in molecular dynamics (MD) simulations, numerous enhanced sampling methods have been developed to expedite the exploration of complex free energy landscapes. A commonly employed approach accelerates the sampling of degrees of freedom associated with pre-defined collective variables (CVs), which typically tends to traverse the entire CV range. However, in many scenarios, the focus of interest is on specific regions within the CV space. This paper introduces a novel "sinking" approach that enables enhanced sampling of arbitrary areas within the CV space. We begin by proposing a gridded convolutional approximation that productively replicates the effects of metadynamics, a powerful CV-based enhanced sampling technique. Building on this, we present the SinkMeta method, which "sinks" the interior bias potential to create restraining potential "cliffs" at the grid edges. This technique can confine the exploration of CVs in MD simulations to a preset area. Our experimental results demonstrate that SinkMeta requires minimal sampling steps to estimate the free energy landscape for CV subspaces of various shapes and dimensions, including irregular two-dimensional regions and one-dimensional pathways between metastable states. We believe that SinkMeta will pioneer a new paradigm for sampling partial phase spaces, especially offering an efficient and flexible solution for sampling minimum free energy paths in high-dimensional spaces.

physics.comp-ph↗

arXiv2024

A Generalized Nucleation Theory for Ice Crystallization

Despite the simplicity of the water molecule, the kinetics of ice nucleation under natural conditions can be complex. We investigated spontaneously grown ice nuclei using all-atom molecular dynamics simulations and found significant differences between the kinetics of ice formation through spontaneously formed and ideal nuclei. Since classical nucleation theory can only provide a good description of ice nucleation in ideal conditions, we propose a generalized nucleation theory that can better characterize the kinetics of ice crystal nucleation in general conditions. This study provides an explanation on why previous experimental and computational studies have yielded widely varying critical nucleation sizes.

cond-mat.soft↗

arXiv2024

Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer

Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical calculations is the most commonly used method. However, this way is heavily dependent on individual experience and chemical intuition. In our previous study, we proposed a research paradigm that uses enhanced sampling in molecular dynamics simulations to study chemical reactions. This approach can directly simulate the entire process of a chemical reaction. However, the computational speed limits the use of high-precision potential energy functions for simulations. To address this issue, we present a scheme for training high-precision force fields for molecular modeling using a previously developed graph-neural-network-based molecular model, molecular configuration transformer. This potential energy function allows for highly accurate simulations at a low computational cost, leading to more precise calculations of the mechanism of chemical reactions. We applied this approach to study a Claisen rearrangement reaction and a Carbonyl insertion reaction catalyzed by Manganese.

physics.chem-ph↗

arXiv2023

Molecular CT: Unifying Geometry and Representation Learning for Molecules at Different Scales

Deep learning is changing many areas in molecular physics, and it has shown great potential to deliver new solutions to challenging molecular modeling problems. Along with this trend arises the increasing demand of expressive and versatile neural network architectures which are compatible with molecular systems. A new deep neural network architecture, Molecular Configuration Transformer (Molecular CT), is introduced for this purpose. Molecular CT is composed of a relation-aware encoder module and a computationally universal geometry learning unit, thus able to account for the relational constraints between particles meanwhile scalable to different particle numbers and invariant with respect to the trans-rotational transforms. The computational efficiency and universality make Molecular CT versatile for a variety of molecular learning scenarios and especially appealing for transferable representation learning across different molecular systems. As examples, we show that Molecular CT enables representational learning for molecular systems at different scales, and achieves comparable or improved results on common benchmarks using a more light-weighted structure compared to baseline models.

cs.LG↗

arXiv2023

Unsupervisedly Prompting AlphaFold2 for Few-Shot Learning of Accurate Folding Landscape and Protein Structure Prediction

Data-driven predictive methods which can efficiently and accurately transform protein sequences into biologically active structures are highly valuable for scientific research and medical development. Determining accurate folding landscape using co-evolutionary information is fundamental to the success of modern protein structure prediction methods. As the state of the art, AlphaFold2 has dramatically raised the accuracy without performing explicit co-evolutionary analysis. Nevertheless, its performance still shows strong dependence on available sequence homologs. Based on the interrogation on the cause of such dependence, we presented EvoGen, a meta generative model, to remedy the underperformance of AlphaFold2 for poor MSA targets. By prompting the model with calibrated or virtually generated homologue sequences, EvoGen helps AlphaFold2 fold accurately in low-data regime and even achieve encouraging performance with single-sequence predictions. Being able to make accurate predictions with few-shot MSA not only generalizes AlphaFold2 better for orphan sequences, but also democratizes its use for high-throughput applications. Besides, EvoGen combined with AlphaFold2 yields a probabilistic structure generation method which could explore alternative conformations of protein sequences, and the task-aware differentiable algorithm for sequence generation will benefit other related tasks including protein design.

cs.LG↗

arXiv2021

Atomistic View of Homogeneous Nucleation of Water into Polymorphic Ices

Water is one of the most abundant substances on Earth, and ice, i.e., solid water, has more than 18 known phases. Normally ice in nature exists only as Ice Ih, Ice Ic, or a stacking disordered mixture of both. Although many theoretical efforts have been devoted to understanding the thermodynamics of different ice phases at ambient temperature and pressure, there still remains many puzzles. We simulated the reversible transitions between water and different ice phases by performing full atom molecular dynamics simulations. Using the enhanced sampling method MetaITS with the two selected X-ray diffraction peak intensities as collective variables, the ternary phase diagrams of liquid water, ice Ih, ice Ic at multiple were obtained. We also present a simple physical model which successfully explains the thermodynamic stability of ice. Our results agree with experiments and leads to a deeper understanding of the ice nucleation mechanism.

cond-mat.stat-mech↗

arXiv2020

Deep Reinforcement Learning of Transition States

Combining reinforcement learning (RL) and molecular dynamics (MD) simulations, we propose a machine-learning approach (RL$^‡$) to automatically unravel chemical reaction mechanisms. In RL$^‡$, locating the transition state of a chemical reaction is formulated as a game, where a virtual player is trained to shoot simulation trajectories connecting the reactant and product. The player utilizes two functions, one for value estimation and the other for policy making, to iteratively improve the chance of winning this game. We can directly interpret the reaction mechanism according to the value function. Meanwhile, the policy function enables efficient sampling of the transition paths, which can be further used to analyze the reaction dynamics and kinetics. Through multiple experiments, we show that RL‡ can be trained tabula rasa hence allows us to reveal chemical reaction mechanisms with minimal subjective biases.

physics.chem-ph↗

arXiv2020

A Perspective on Deep Learning for Molecular Modeling and Simulations

Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in molecular modeling and simulations is still at an early stage, largely because the inductive biases of molecules are completely different from those of images or texts. Footed on these differences, we first reviewed the limitations of traditional deep learning models from the perspective of molecular physics, and wrapped up some relevant technical advancement at the interface between molecular modeling and deep learning. We do not focus merely on the ever more complex neural network models, instead, we emphasize the theories and ideas behind modern deep learning. We hope that transacting these ideas into molecular modeling will create new opportunities. For this purpose, we summarized several representative applications, ranging from supervised to unsupervised and reinforcement learning, and discussed their connections with the emerging trends in deep learning. Finally, we outlook promising directions which may help address the existing issues in the current framework of deep molecular modeling.

physics.comp-ph↗

arXiv2019

Learning Clustered Representation for Complex Free Energy Landscapes

In this paper we first analyzed the inductive bias underlying the data scattered across complex free energy landscapes (FEL), and exploited it to train deep neural networks which yield reduced and clustered representation for the FEL. Our parametric method, called Information Distilling of Metastability (IDM), is end-to-end differentiable thus scalable to ultra-large dataset. IDM is also a clustering algorithm and is able to cluster the samples in the meantime of reducing the dimensions. Besides, as an unsupervised learning method, IDM differs from many existing dimensionality reduction and clustering methods in that it neither requires a cherry-picked distance metric nor the ground-true number of clusters, and that it can be used to unroll and zoom-in the hierarchical FEL with respect to different timescales. Through multiple experiments, we show that IDM can achieve physically meaningful representations which partition the FEL into well-defined metastable states hence are amenable for downstream tasks such as mechanism analysis and kinetic modeling.

cond-mat.stat-mech↗

arXiv2019

Homogeneous nucleation of ice

Ice nucleation is a process of great relevance in physics, chemistry, technology and environmental sciences, much theoretical and experimental efforts have been devoted to its understanding, but still it remains a topic of intense research. We shed light on this phenomenon by performing atomistic based simulations. Using metadynamics and a carefully designed set of collective variables, reversible transitions between water and ice are able to be simulated. We find that water freezes into a stacking disordered structure with the all-atom TIP4P/Ice model, and the features of the critical nucleus of nucleation at the microscopic level are revealed. Our results are in agreement with recent experimental and other theoretical works and confirm that nucleation is preceded by a large increase in tetrahedrally coordinated water molecules.

cond-mat.soft↗

arXiv2018

Combining Metadynamics and Integrated Tempering Sampling

The simulation of rare events is one of the key problems in atomistic simulations. Towards its solution a plethora of methods have been proposed. Here we combine two such methods metadynamics and inte-grated tempering sampling. In metadynamics the fluctuations of a carefully chosen collective variable are amplified, while in integrated tempering sampling the system is pushed to visit an approximately uniform interval of energies and allows exploring a range of temperatures in a single run. We describe our ap-proach and apply it to the two prototypical systems a SN2 chemical reaction and to the freezing of silica. The combination of metadynamics and integrated tempering sampling leads to a powerful method. In par-ticular in the case of silica we have measured more than one order of magnitude acceleration.

physics.chem-ph↗