Related papers: A Theoretical Examination of Diffusive Molecular D…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
The mechanism of diffusing diffusivity predicts that, in environments where the diffusivity changes gradually, the displacement distribution becomes non-Gaussian, even though the mean-squared displacement (MSD) grows linearly with time.…
A generalized formalism of the so-called non-adiabatic quantum molecular dynamics is presented, which applies for atomic many-body systems in external laser fields. The theory treats the nuclear dynamics and electronic transitions…
We describe the crossover from generalized hydrodynamics to conventional hydrodynamics in nearly integrable systems. Integrable systems have infinitely many conserved quantities, which spread ballistically in general. When integrability is…
These are lecture notes for various Summer and Winter schools that I have given. The notes describe the methodology called Variational Modelling, and focus on the application to the modelling of gradient-flow systems. I describe the…
We develop a novel approach for the construction of quantile processes governing the stochastic dynamics of quantiles in continuous time. Two classes of quantile diffusions are identified: the first, which we largely focus on, features a…
Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…
We present a multiscale simulation algorithm for amorphous materials, which we illustrate and validate in a canonical case of dense granular flow. Our algorithm is based on the recently proposed Spot Model, where particles in a dense random…
The dynamical properties of classical fluids at pico-liter scale attract experimentally and theoretically much attention in the soft-matter and biophysics communities, due to the appearance of the microfluidics, also called 'lab-on-a-chip',…
Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a…
We study the spreading of a quantum-mechanical wavepacket in a one-dimensional tight-binding model with a noisy potential, and analyze the emergence of classical diffusion from the quantum dynamics due to decoherence. We consider a finite…
We present extensive molecular dynamics simulations of the motion of a single linear rigid molecule in a two-dimensional random array of fixed obstacles. The diffusion constant for the center of mass translation, $D_{\rm CM}$, and for…
In this paper, we introduce a diffuse interface model for describing the dynamics of mixtures involving multiple (two or more) phases. The coupled hydrodynamical system is derived through an energetic variational approach. The total energy…
The diffusing-diffusivity mechanism proposed by Chubynsky and Slater [PRL 113, 098302, 2014] predicts that, in environments where the diffusivity changes gradually, the displacement distribution becomes non-Gaussian, even though the…
Machine learning (ML) methods provide advanced means for understanding inherent patterns within large and complex datasets. Here, we employ the principal component analysis (PCA) and the diffusion map (DM) techniques to evaluate the glass…
Diffusion in a multidimensional energy surface with minima and barriers is a problem of importance in statistical mechanics and also has wide applications, such as protein folding. To understand it in such a system, we carry out theory and…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
Wang et al. [PNAS 106 (2009) 15160] have found that in several systems the linear time dependence of the mean-square displacement (MSD) of diffusing colloidal particles, typical of normal diffusion, is accompanied by a non-Gaussian…
We introduce the concept of Randomly Modulated Gaussian Processes as a unifying framework for modeling, analyzing and classifying anomalous diffusion models in heterogeneous media. This formulation incorporates correlations in the…
A diffusion process for charge distributions in a phase space is examined. The corresponding charge moves in a force field and under an action of a random field. There are the diffusion motions for coordinates and for momenta. In our model,…