Related papers: Shadow Molecular Dynamics for Flexible Multipole M…
Dark energy is one of the deepest puzzles in modern cosmology, and mounting evidence suggests that it is not just a cosmological constant but a genuinely dynamical component. Although cosmology and dynamical systems theory emerged from…
While it is commonly observed that the shape dynamics of mammalian cells can undergo large random fluctuations, theoretical models aiming at capturing cell mechanics often focus on the deterministic part of the motion. In this paper, we…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
While a scalar field with a pole in its kinetic term is often used to study the cosmological inflation, it can also play the role of dark energy, which is called the pole dark energy model. We propose a generalized model that the scalar…
Experimental studies of systems containing active proteins that undergo conformational changes driven by catalytic chemical reactions have shown that the diffusion coefficients of passive tracer particles and active molecules are larger…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Understanding the quantum dynamics of strongly coupled molecule-cavity systems remains a significant challenge in molecular polaritonics. This work develops a comprehensive self-consistent model simulating electromagnetic interactions of…
Differentiable physics is a powerful approach to learning and control problems that involve physical objects and environments. While notable progress has been made, the capabilities of differentiable physics solvers remain limited. We…
We investigate the cosmological dynamics of the recently proposed extended chameleon models at both background and linear perturbation levels. Dynamical systems techniques are employed to fully characterize the evolution of the universe at…
We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of spherical colloidal particles. The solvent is modeled on the level of the lattice-Boltzmann method while the…
Neural-based, data-driven analysis and control of dynamical systems have been recently investigated and have shown great promise, e.g. for safety verification or stability analysis. Indeed, not only do neural networks allow for an entirely…
We propose a computational method to simulate anomalous self-diffusion in a simple liquid. The method is based on a molecular dynamics simulation on which we impose the following two conditions: firstly, the inter-particle interaction is…
We numerically study the energy transfer in a multi-component $2d$ film, made of an active polar gel and a passive isotropic fluid in presence of surfactant favoring emulsification. We show that by confining the active behavior into the…
To evaluate electrostatics interactions, Molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM)…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Motivated by a similar approach for Born-Oppenheimer molecular dynamics, this paper proposes an extended "shadow" Lagrangian density for quantum states of superfluids. The extended Lagrangian contains an additional field variable that is…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
We systematically investigate the existence, stability, and propagation dynamics of multipole-mode (necklace-shaped) solitons in the two-dimensional model of an optical medium with the defocusing saturable nonlinearity and an annular…