Related papers: Segmental Lennard-Jones Interactions for Semi-flex…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
In this paper we explore how concepts of high-dimensional data compression via random projections onto lower-dimensional spaces can be applied for tractable simulation of certain dynamical systems modeling complex interactions. In such…
We propose a 2-d computational model-system comprising a mixture of spheres and the objects of some other shapes, interacting via the Lennard-Jones potential. We propose a reliable and efficient numerical algorithm to obtain void…
We introduce a nonparametric algorithm to learn interaction kernels of mean-field equations for 1st-order systems of interacting particles. The data consist of discrete space-time observations of the solution. By least squares with…
We study fluid structure and water-like anomalies of a system constituted by dimeric particles interacting via a purely repulsive core-softened potential by means of integral equation theories. In our model, dimers interact through a…
We compare two approaches in modeling repulsive interactions among hadrons: the excluded volume approximation and the S-matrix formalism. These are applied to study the thermodynamics of the $\pi N \Delta$ system. It is shown that the…
Polarized neutron reflectometry (PNR) have developed theoretically and experimentally in the past decades. In order to resolve the phase problem in neutron reflectometry, several simulation methods have been proposed such as reference layer…
Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This…
We present a numerical solution of the Worm-Like Chain (WLC) model for semi-flexible polymers. We display graphs for the end-to-end distance distribution and the force-extension relation expected from the model. We predict the expected…
The contamination, or background, from uninteresting low-energy strong interactions is a major issue for data analysis at the Large Hadron Collider. In the light of the challenges associated with the upcoming higher-luminosity scenarios,…
Physics-based simulation is essential for developing and evaluating robot manipulation policies, particularly in scenarios involving deformable objects and complex contact interactions. However, existing simulators often struggle to balance…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
Systems of interacting particles or agents have wide applications in many disciplines such as Physics, Chemistry, Biology and Economics. These systems are governed by interaction laws, which are often unknown: estimating them from…
A microscopic model of a surface polymer network - membrane system is introduced, with contact polymer surface interactions that can be either repulsive or attractive and sliplinks of functionality four randomly distributed over the…
We simulate model systems of charged spherical particles in their counterion solution and measure the thermodynamic pressure and the pair distribution function from which we derive effective potentials of mean force. For a system with only…
Reptation theory has been highly successful in explaining the unusual material properties of entangled polymer solutions. It reduces the complex many-body dynamics to a single-polymer description where each polymer is envisaged to be…
We study the mechanical and conformational properties of networks of helical polymers with a combination of Monte Carlo simulations based on the Wang-Landau algorithm and the Three-chain Model. We find that the stress-strain behavior of…
We present LayerPCM, an extension of the polarizable-continuum model coupled to real-time time-dependent density-functional theory for an efficient and accurate description of the electrostatic interactions between molecules and…
The phase behavior of rodlike molecules with polydisperse length and solvent-mediated attraction and repulsion is described by an extension of the Onsager theory for rigid rods. A phenomenological square-well potential is used to model…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…