Related papers: Molecular dynamics simulations of complex shaped p…
The ability to perform ab initio molecular dynamics simulations using potential energies calculated on quantum computers would allow virtually exact dynamics for chemical and biochemical systems, with substantial impacts on the fields of…
Molecular dynamics simulations are indispensable for exploring the behavior of atoms and molecules. Grounded in quantum mechanical principles, quantum molecular dynamics provides high predictive power but its computational cost is dominated…
Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…
Molecular Dynamic (MD) approach is applied to study the converging cylindrical shock waves in a dense Lennard-Jones (LJ) fluid. MD method is based on tracking of the atom motions and hence it has an fundamental advantages over hydrodynamic…
We propose a neural operator framework, termed mixture density nonlinear manifold decoder (MD-NOMAD), for stochastic simulators. Our approach leverages an amalgamation of the pointwise operator learning neural architecture nonlinear…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Higher-rank Minkowski valuations are efficient means for describing the geometry and connectivity of spatial patterns. We show how to extend the framework of the scalar Minkowski valuations to vector- and tensor-valued measures. The…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for…
The modeling of atomistic biomolecular simulations using kinetic models such as Markov state models (MSMs) has had many notable algorithmic advances in recent years. The variational principle has opened the door for a nearly fully automated…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
A real-space formalism for density-functional perturbation theory (DFPT) is derived and applied for the computation of harmonic vibrational properties in molecules and solids. The practical implementation using numeric atom-centered…
Special stochastic representation of the wave function in Quantum Mechanics (QM), based on soliton realization of extended particles, is suggested with the aim to model quantum states via classical computer. Entangled solitons construction…
We explore the connection between the four-dimensional Minkowski-space Bethe-Salpeter equation and its light-front projection, emphasizing the implications for bound-state dynamics. Our approach incorporates dressed particles, such as…
A new physical implementation for quantum computation is proposed. The vibrational modes of molecules are used to encode qubit systems. Global quantum logic gates are realized using shaped femtosecond laser pulses which are calculated…
An extended Wigner function formalism is introduced for describing the quantum dynamics of particles with internal degrees of freedom in the presence of spatially inhomogeneous fields. The approach is used for quantitative simulations of…
There is an increasing demand for computing the relevant structures, equilibria and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ…
Massive spinning particle in $6d$-Minkowski space is described as a mechanical system with the configuration space $R^{5,1} \times CP^3$. The action functional of the model is unambiguously determined by the requirement of identical…
Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. can be formed dynamically from hot…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…