Related papers: Automatic Coarse Graining of Polymers
Boltzmann samplers and the recursive method are prominent algorithmic frameworks for the approximate-size and exact-size random generation of large combinatorial structures, such as maps, tilings, RNA sequences or various tree-like…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
We present a new reduced-order computational method for the molecular dynamics simulation of entangled polymer systems. The polymer chains are modeled as continuous Gaussian chains. Our algorithm is based on the application of the molecular…
The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several…
A coarse-graining strategy for dilute and semi-dilute solutions of interacting polymers, and of colloid polymer mixtures is briefly described. Monomer degrees of freedom are traced out to derive an effective, state dependent pair potential…
The task of finding the optimal compression of a polyline with straight-line segments and arcs is performed in many applications, such as polyline compression, noise filtering, and feature recognition. Optimal compression algorithms find…
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…
We develop a systematic coarse graining procedure for systems of $N$ qubits. We exploit the underlying geometrical structures of the associated discrete phase space to produce a coarse-grained version with reduced effective size. Our…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
We study multilevel techniques, commonly used in PDE multigrid literature, to solve structured optimization problems. For a given hierarchy of levels, we formulate a coarse model that approximates the problem at each level and provides a…
Scale analysis based on coarse-graining has been proposed recently as an alternative to Fourier analysis. It is now broadly used to analyze energy spectra and energy transfers in eddy-resolving ocean simulations. However, for data from…
With the birth of quantum information science, many tools have been developed to deal with many-body quantum systems. Although a complete description of such systems is desirable, it will not always be possible to achieve this goal, as the…
Coarse-grained simulations of conjugated polymers have become a popular way of investigating the device physics of organic photovoltaics. While UV-Vis spectroscopy remains one of key experimental methods for the interrogation of these…
For a wide range of phenomena, current computational ability does not always allow for fully atomistic simulations of high-dimensional molecular systems to reach time scales of interest. Coarse-graining (CG) is an established approach to…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
This thesis introduces a framework that is able to describe general many-body coarse-grained interactions. We make use of this to describe the free energy surface as a cluster expansion in terms of monomer, dimer, and trimer terms. The…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
We propose a coarse-grained picture to control ``complex'' quantum dynamics, i.e., multi-level-multi-level transition with a random interaction. Assuming that optimally controlled dynamics can be described as a Rabi-like oscillation between…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…