Related papers: GMXPolymer: a generated polymerization algorithm b…
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…
We present a new integral transform called the Generalized Borel Transform (GBT) and show how to use it to compute some distribution functions used to describe the statistico-mechanical behavior of macromolecules. For this purpose, we…
In this work we introduce a geometric integrator for molecular dynamics simulations of physical systems in the canonical ensemble. In particular, we consider the equations arising from the so-called density dynamics algorithm with any…
Polymer composite materials require softening to reduce their glass transition temperature and improve processability. To this end, plasticizers, which are small organic molecules, are added to the polymer matrix. The miscibility of these…
We review recent results from computer simulation studies of polymer glasses, from chain dynamics around the glass transition temperature Tg to the mechanical behaviour below Tg. These results clearly show that modern computer simulations…
We investigate a novel non-parametric regression-based clustering algorithm for longitudinal data analysis. Combining natural cubic splines with Gaussian mixture models (GMM), the algorithm can produce smooth cluster means that describe the…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
We present a general formalism able to derive the kinetic equations of polymer dynamics. It is based on the application of nonequilibrium thermodynamics to analyze the irreversible processes taking place in the conformational space of the…
Polymers are a versatile class of materials with widespread industrial applications. Advanced computational tools could revolutionize their design, but their complex, multi-scale nature poses significant modeling challenges. Conventional…
A challenging topic in materials engineering is the development of numerical models that can accurately predict material properties with atomistic accuracy, matching the scale and level of detail achieved by experiments. In this regard,…
While the structural dynamics of chromophores are of interest for a range of applications, it is experimentally very challenging to resolve the underlying microscopic mechanisms. Glassy dynamics are also challenging for atomistic…
Active polymers are ubiquitous in nature, and often kicked by persistent noises that break detailed balance. In order to capture the out-of-equilibrium dynamics of such active polymers, we propose a simple yet reliable analytical framework…
A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…
Self-supervised neural language models have recently found wide applications in generative design of organic molecules and protein sequences as well as representation learning for downstream structure classification and functional…
Polymers, macromolecules formed from covalently bonded monomers, underpin countless technologies and are indispensable to modern life. While deep learning is advancing polymer science, existing methods typically represent the whole polymer…
A strategy is developed for generating equilibrated high molecular-weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains…
From the relative scarcity of training data to the lack of standardized benchmarks, the development of foundation models for polymers face significant and multi-faceted challenges. At the core, many of these issues are tied directly to the…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
We introduce an iterative method named GPMR for solving 2x2 block unsymmetric linear systems. GPMR is based on a new process that reduces simultaneously two rectangular matrices to upper Hessenberg form and that is closely related to the…
Symplectic integrators for Hamiltonian systems have been quite successful for studying few-body dynamical systems. These integrators are frequently derived using a formalism built on symplectic maps. There have been recent efforts to extend…