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Force-matched water models provide a practical route from first-principles reference data to long classical and path-integral molecular simulations. Previous flexible four-site potentials in the spirit of q-TIP4P/F showed that fitting…
The ultra-cold and weakly-coupled Fermi gas in two spatial dimensions is studied in an effective field theory framework. It has long been observed that universal corrections to the energy density to two orders in the interaction strength do…
Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, existing methods still face key limitations: classical…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Due to the complex characteristics of bottle-brush polymers, it became a challenge to develop an efficient algorithm for studying such macromolecules under various solvent conditions or some constraints in the space by using computer…
In a recent paper, J. Chem. Phys. 162, 214101 (2025), a novel approach for the rigidification of a molecular cluster was proposed, in which starting with an all-atom (AA) potential, a coarse-grained (CG) potential for the associated cluster…
The Generalized Fermi Breakup recently demonstrated to be formally equivalent to the Statistical Multifragmentation Model, if the contribution of excited states are included in the state densities of the former, is implemented. Since this…
Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic…
Exact characterization of phase transitions requires sufficient configurational sampling, necessitating efficient and accurate potential energy surfaces. Molecular force fields with computational efficiency and physical interpretability are…
We extend a phase-field/gradient damage formulation for cohesive fracture to the dynamic case. The model is characterized by a regularized fracture energy that is linear in the damage field, as well as non-polynomial degradation functions.…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
The influence of microscopic force fields on the motion of Brownian particles plays a fundamental role in a broad range of fields, including soft matter, biophysics, and active matter. Often, the experimental calibration of these force…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…
An ordinary state-based peridynamic material model is proposed for single sheet graphene. The model is calibrated using coarse grained molecular dynamics simulations. The coarse graining method allows the dependence of bond force on bond…
In this article we introduce the MARTINI model of a widely used thermoresponsive polymer, Poly(N-isopropylacrylamide). Importantly, our model takes into account polymer's stereoregularity (i.e. tacticity). We highlight the effect of…
Molecular dynamics is a valuable tool to probe biological processes at the atomistic level - a resolution often elusive to experiments. However, the credibility of molecular models is limited by the accuracy of the underlying force field,…
In this chapter we introduce a combined parameter and model reduction methodology and present its application to the efficient numerical estimation of a pressure drop in a set of deformed carotids. The aim is to simulate a wide range of…
In this paper, a novel isogeometric method for Biot's consolidation model is constructed and analyzed, using a four-field formulation where the unknown variables are the solid displacement, solid pressure, fluid flux, and fluid pressure.…