Related papers: Resolution limit of data-driven coarse-grained mod…
The computational study of the interaction between charged, ligand-protected metal nanoparticles and model lipid membranes has been recently addressed both at atomistic and coarse grained level. Here we compare the performance of three…
Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…
The Single Chain Mean Field theory is used to simulate the equilibrium structure of phospholipid membranes at the molecular level. Three levels of coarse-graining of DMPC phospholipid surfactants are present: the detailed 44-beads double…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…
Models often need to be constrained to a certain size for them to be considered interpretable. For example, a decision tree of depth 5 is much easier to understand than one of depth 50. Limiting model size, however, often reduces accuracy.…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
The growing size of neural language models has led to increased attention in model compression. The two predominant approaches are pruning, which gradually removes weights from a pre-trained model, and distillation, which trains a smaller…
We present a systematic coarse-graining (CG) strategy for many particle molecular systems based on cluster expansion techniques. We construct a hierarchy of coarse-grained Hamiltonians with interaction potentials consisting of two, three…
We present a simple model which allows to investigate equilibrium aspects of molecular recognition between rigid biomolecules on a generic level. Using a two-stage approach, which consists of a design and a testing step, the role of…
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of…
In this study, a coarse-graining framework for discrete models is formulated on the basis of multiscale homogenization. The discrete model considered in this paper is the Lattice Discrete Particle Model (LDPM), which simulates concrete at…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
In this work, we present a method to generate a configurational level fingerprint for polymers using the Bead-Spring-Model. Unlike some of the previous fingerprinting approaches that employ monomer-level information where atomistic…
The properties of soft electronic materials depend on the coupling of electronic and conformational degrees of freedom over a wide range of spatiotemporal scales. Description of such properties requires multiscale approaches capable of, at…
In this paper, we present a new coarse-grained (CG) model for poly (alpha-peptoid)s that is compatible with the MARTINI CG FF. In the proposed model, CG poly (alpha-peptoid) is composed by a CG backbone (here we select polysarcosine as the…