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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…
In this work, we consider pressurized phase-field fracture problems in nearly and fully incompressible materials. To this end, a mixed form for the solid equations is proposed. To enhance the accuracy of the spatial discretization, a…
A simulation can stand its ground against experiment only if its prediction uncertainty is known. The unknown accuracy of interatomic potentials (IPs) is a major source of prediction uncertainty, severely limiting the use of large-scale…
Impact crater experiments in granular media traditionally involve loosely packed sand targets. However, this study investigates granular impact craters on both loosely and more tightly packed sand targets. We report granular vs. granular…
The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…
Accurate estimation of mutational effects on protein-protein binding energies is an open problem with applications in structural biology and therapeutic design. Several deep learning predictors for this task have been proposed, but,…
Experimental measurements in collisions of small systems from p+p to p/d/3He+A at RHIC and the LHC reveal particle emission patterns that are strikingly similar to those observed in A+A collisions. One explanation of these patterns is the…
Compressing or cooling a fluid typically enhances its static interparticle correlations. However, there are notable exceptions. Isothermal compression can reduce the translational order of fluids that exhibit anomalous waterlike trends in…
To enhance the reflectivity of X-ray mirrors beyond the critical angle, multilayer coatings are required. Interface imperfections in the multilayer growth process are known to cause non-specular scattering and degrade the mirror optical…
The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the…
We have performed all atom molecular dynamics simulations on the projection domain of the intrinsically disordered htau40 protein. After generating a suitable ensemble of starting conformations at high temperatures, at room temperature in…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…
Molecular dynamics (MD) simulations give access to equilibrium structures and dynamic properties given an ergodic sampling and an accurate force-field. The force-field parameters are calibrated to reproduce properties measured by…
We discuss capability of Smooth Particle Hydrodynamics to represent adequately the dynamics of self-gravitating systems, in particular for what regards the quality of approximation of force fields in the motion equations. When cubic spline…
Soft materials may break irreversibly upon applying sufficiently large shear oscillations, a process which physical mechanism remains largely elusive. In this work, the rupture of protein gels made of sodium caseinate under an oscillatory…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
Time-resolved scattering experiments enable imaging of materials at the molecular scale with femtosecond time resolution. However, in disordered media they provide access to just one radial dimension thus limiting the study of orientational…
Given that the physical properties of polymeric liquids extend on a wide range of lengthscales, it is computationally convenient to represent them by coarse-grained (CG) descriptions at various granularities to investigate local and global…