Related papers: Coarse-graining strategies in polymer solutions
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is studied for various chain lengths and grafting densities under good solvent conditions, by Molecular Dynamics methods and density functional…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…
We present a new computational framework combining coarse-graining techniques with bootstrap methods to study quantum many-body systems. The method efficiently computes rigorous upper and lower bounds on both zero- and finite-temperature…
We study a two-stage mixed-integer linear program (MILP) with more than 1 million binary variables in the second stage. We develop a two-level approach by constructing a semi-coarse model (coarsened with respect to variables) and a coarse…
Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different…
We systematically derive an exact coarse-grained description for interacting particles with thermodynamically consistent stochastic dynamics, applicable across different observation scales, the mesoscopic and the macroscopic. We implement…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
Tailoring the nanoscale distribution of chemical species at grain boundaries is a powerful method to dramatically influence the properties of polycrystalline materials. However, classical approaches to the problem have tacitly assumed that…
We introduce a closure model for coarse-grained kinetic theories of polar active fluids. Based on a quasi-equilibrium approximation of the particle distribution function, the model closely captures important analytical properties of the…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a…
We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often…
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…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square…
We present the state-of-the-art theoretical modeling, molecular simulation, and coarse-graining strategies for the transport of gases and liquids in nanoporous materials (pore size 1-100 nm). Special emphasis is placed on the transport of…
The complexity of biomolecular interactions necessitates advanced methodologies to accurately capture their behavior in solution. In this work, we focus on monoclonal antibodies and adopt a multi-scale coarse-graining strategy for their…
A new method is introduced to simulate jamming of polyhedral grains under controlled stress that incorporates global degrees of freedom through the metric tensor of a periodic cell containing grains. Jamming under hydrostatic/isotropic…