Related papers: Cell List Algorithms for Nonequilibrium Molecular …
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
We present a numerical model and a set of conservative algorithms for Non-Maxwellian plasma kinetics with inelastic collisions. These algorithms self-consistently solve for the time evolution of an isotropic electron energy distribution…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Calculating one-body density profiles in equilibrium via particle-based simulation methods involves counting of events of particle occurrences at (histogram-resolved) space points. Here we investigate an alternative method based on a…
This work proposes a model for granular deformation that predicts the stress and velocity profiles in well-developed dense granular flows. Recent models for granular elasticity (Jiang and Liu 2003) and rate-sensitive plastic flow (Jop et…
Two effective methods for writing the dynamical equations for non-holonomic systems are illustrated. They are based on the two types of representation of the constraints: by parametric equations or by implicit equations. They can be applied…
In applied sciences, we often deal with deterministic simulation models that are too slow for simulation-intensive tasks such as calibration or real-time control. In this paper, an emulator for a generic dynamic model, given by a system of…
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using the Einstein relation, the particle positions need to be…
Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and…
A dynamic graph algorithm is a data structure that answers queries about a property of the current graph while supporting graph modifications such as edge insertions and deletions. Prior work has shown strong conditional lower bounds for…
The Stokeslet and stresslet kernels are commonly used in boundary element simulations and singularity methods for slow viscous flow. Evaluating the velocity induced by a collection of Stokeslets and stresslets by direct summation requires…
We present a simulation workflow for efficient investigations of the interplay between 3D lithium-ion electrode microstructures and electrochemical performance, with emphasis on lithium plating. Our approach addresses several challenges.…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
Machine learning force fields show great promise in enabling more accurate molecular dynamics simulations compared to manually derived ones. Much of the progress in recent years was driven by exploiting prior knowledge about physical…
Carbon isotope labeling method is a standard metabolic engineering tool for flux quantification in living cells. To cope with the high dimensionality of isotope labeling systems, diverse algorithms have been developed to reduce the number…
In the emerging field of 3D bioprinting, cell damage due to large deformations is considered a main cause for cell death and loss of functionality inside the printed construct. Those deformations, in turn, strongly depend on the…
One of the difficulties in 3D reconstruction of molecules from images in single particle Cryo-Electron Microscopy (Cryo-EM), in addition to high levels of noise and unknown image orientations, is heterogeneity in samples: in many cases, the…
In the simulation of biological molecules, it is customary to impose constraints on the fastest degrees of freedom to increase the time step. The evaluation of the involved constraint forces must be performed in an efficient manner, for…
We review a dynamical approach to non-equilibrium MD (D-NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non-equilibrium state produced by a suitable…
We present a set of effective outflow/open boundary conditions and an associated algorithm for simulating the dynamics of multiphase flows consisting of $N$ ($N\geqslant 2$) immiscible incompressible fluids in domains involving outflows or…