Related papers: A Theoretical Examination of Diffusive Molecular D…
We show that the kinetic-theoretical self-diffusion coefficient of an atomic fluid plays the same role as the short-time self-diffusion coefficient D_S in a colloidal liquid, in the sense that the dynamic properties of the former, at times…
The complexities of today's materials simulations demand computer codes which are both powerful and highly flexible. A researcher should be able to readily choose different geometries, different materials and different algorithms without…
Molecular dynamics simulations are carried out to investigate the diffusion behavior of penetrable-sphere model fluids characterized by a finite energy barrier $\epsilon$. The self-diffusion coefficient is evaluated from the time-dependent…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
Applications of variational methods are typically restricted to conservative systems. Some extensions to dissipative systems have been reported too but require ad hoc techniques such as the artificial doubling of the dynamical variables.…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
Confinement can substantially alter the physicochemical properties of materials by breaking translational isotropy and rendering all physical properties position-dependent. Molecular dynamics (MD) simulations have proven instrumental in…
Simulating long-term mass diffusion kinetics with atomic precision is important to predict chemical and mechanical properties of alloys over time scales of engineering interest in applications, including (but not limited to) alloy heat…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
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…
A simple manner to describe the diffusive relaxation of a colloidal fluid adsorbed in a porous medium is to model the porous medium as a set of spherical particles fixed in space at random positions with prescribed statistical structural…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
We propose score dynamics (SD), a general framework for learning accelerated evolution operators with large timesteps from molecular-dynamics simulations. SD is centered around scores, or derivatives of the transition log-probability with…
This work presents a complete geometrical characterisation of divisible and indivisible time-evolution at the level of probabilities for systems with two configurations, open or closed. Our new geometrical construction in the space of…
In the hydrodynamic theory, the non-equilibrium dynamics of a many-body system is approximated, at large scales of space and time, by irreversible relaxation to local entropy maximisation. This results in a convective equation corrected by…
Extracting governing physical laws from computational or experimental data is crucial across various fields such as fluid dynamics and plasma physics. Many of those physical laws are dissipative due to fluid viscosity or plasma collisions.…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
The diffusion equation is the primary tool to study the movement dynamics of a free Brownian particle, but when spatial heterogeneities in the form of permeable interfaces are present, no fundamental equation has been derived. Here we…
Generative diffusion models have achieved remarkable success in producing high-quality images. However, these models typically operate in continuous intensity spaces, diffusing independently across pixels and color channels. As a result,…
Diffusion models are distinguished by their exceptional generative performance, particularly in producing high-quality samples through iterative denoising. While current theory suggests that the number of denoising steps required for…