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We study numerically and analytically the coarsening of stripe phases in two spatial dimensions, and show that transient configurations do not achieve long ranged orientational order but rather evolve into glassy configurations with very…
A discrete-to-continuum analysis for free-boundary problems related to crystalline films deposited on substrates is performed by $\Gamma$-convergence. The discrete model here introduced is characterized by an energy with two contributions,…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation…
This paper investigates the behavior of a heavy soft spring in steady circular motion. Since the spring is inhomogeneous due to centrifugal force, one can rigorously prove that it follows the one-dimensional static Willis-form equations.…
We simulate a densely jammed, athermal assembly of repulsive soft particles immersed in a solvent. Starting from an initial condition corresponding to a quench from a high temperature, we find non-trivial slow dynamics driven by a gradual…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
Understanding the activity of large populations of neurons is difficult due to the combinatorial complexity of possible cell-cell interactions. To reduce the complexity, coarse-graining had been previously applied to experimental neural…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied using two theoretical approaches. One is the equilibrium simulation approach with quantum…
Efficient sampling of the Boltzmann distribution of molecular systems is a long-standing challenge. Recently, instead of generating long molecular dynamics simulations, generative machine learning methods such as normalizing flows have been…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
We perform computer simulations of a Cahn-Hilliard model of phase separation which has dynamical asymmetry between the two coexisting phases. The dynamical asymmetry is incorporated by considering a mobility function which is order…
We consider conformation dynamics of a chain-like three-body bead-spring model, in which three point masses are connected in series by two springs and the conformation is defined by the bending angle between the two springs. Previous…
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during…
An important class of fluid-structure problems involve the dynamics of ordered arrays of immersed, flexible fibers. While specialized numerical methods have been developed to study fluid-fiber systems, they become infeasible when there are…
We discuss in details a modified variational matrix-product-state algorithm for periodic boundary conditions, based on a recent work by P. Pippan, S.R. White and H.G. Everts, Phys. Rev. B 81, 081103(R) (2010), which enables one to study…
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the…
We study the elastic response of concentrated suspensions of rigid wire frame particles to a step strain. These particles are constructed from infinitely thin, rigid rods of length $L$. We specifically compare straight rod-like particles to…