Related papers: LAMMPS Framework for Dynamic Bonding and an Applic…
Domain-driven design (DDD) is a powerful design technique for architecting complex software systems. This paper introduces a prompting framework that automates core DDD activities through structured large language model (LLM) interactions.…
Force field-based molecular dynamics (MD) simulations are indispensable for probing the structure, dynamics, and functions of biomolecular systems, including proteins and protein-ligand complexes. Despite their broad utility in drug…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
Evaluating large language models (LLMs) today rests on fixed benchmarks that apply the same set of items to any model, producing ceiling and floor effects that mask capability gaps. We argue that the most informative evaluation signal lies…
Contemporary materials science research is heavily conducted in silico, involving massive simulations of the atomic-scale evolution of materials. Cataloging basic patterns in the atomic displacements is key to understanding and predicting…
We propose a technique to detect and generate patterns in a network of locally interacting dynamical systems. Central to our approach is a novel spatial superposition logic, whose semantics is defined over the quad-tree of a partitioned…
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…
Biological adhesion often involves several pairs of specific receptor-ligand molecules. Using rate equations, we study theoretically the rupture of such multiple parallel bonds under dynamic loading assisted by thermal activation. For a…
A multi-resolution bead-spring model for polymer dynamics is developed as a generalization of the Rouse model. A polymer chain is described using beads of variable sizes connected by springs with variable spring constants. A numerical…
DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages…
We introduce GlassMLP, a machine learning framework using physics-inspired structural input to predict the long-time dynamics in deeply supercooled liquids. We apply this deep neural network to atomistic models in 2D and 3D. Its performance…
This work proposes the Lattice Boltzmann Model (LBM) to learn real-world pixel dynamicity for visual tracking. LBM decomposes visual representations into dynamic pixel lattices and solves pixel motion states through collision-streaming…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language…
The rapid evolution of large language models (LLMs) has transformed conversational agents, enabling complex human-machine interactions. However, evaluation frameworks often focus on single tasks, failing to capture the dynamic nature of…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
Predicting the rheological behavior of associative polymers bridging colloidal particles into transient networks is fundamentally challenging because the coupled spatiotemporal scales prevent efficient molecular-fidelity modeling. We…
This paper presents a proposal of a rather new type of effective interatomic interaction for molecular dynamics and similar applications. The model consists of atoms with prescribed geometric arrangement of active orbitals, represented by…
The pseudopotential model within the Lattice Boltzmann Method (LBM) framework has emerged as a prominent approach in computational fluid dynamics due to its dual strengths in physical intuitiveness and computational tractability. However,…