Related papers: Computing and Bounding Equilibrium Concentrations …
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
We perform a thermodynamic analysis of the polymerization-induced phase separation in nanoparticle-monomer-polymer blends using a simple model recently proposed by V. V. Ginzburg (Macromolecules 2005, 38, 2362.). The model was adapted for…
The detailed balance property is a fundamental property that must be satisfied in all the macroscopic systems with a well defined temperature at each point. On the other hand, many biochemical networks work in non-equilibrium conditions and…
Geopolymers are an emerging class of binding materials used in sustainable cements, concretes, and composites. However, despite growing research, the lack of standardised processes and stability analyses for formulating activator solutions…
Active polymeric systems exhibit a rich spectrum of non-equilibrium phenomena arising from stochastic forces that explicitly break detailed balance. Despite the rapid growth of experimental and numerical studies, analytical progress remains…
We consider the statistical mechanics of a system of topologically linked polymers, such as for instance a dense solution of polymer rings. If the possible topological states of the system are distinguished using the Gauss linking number as…
We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to…
High-throughput computational screening of polymers offers a powerful way to address the imbalance between the vast number of polymers synthesised for diverse applications and the relatively small subset that can be studied using atomistic…
We present the complete phase diagram for one-dimensional binary mixtures of bosonic ultracold atomic gases in a harmonic trap. We obtain exact results with direct numerical diagonalization for small number of atoms, which permits us to…
During fast diffusion-influenced polymerization, nonequilibrium behavior of the polymer chains and the surrounding reactive monomers has been reported recently. Based on the laws of thermodynamics, the emerging nonequilibrium structures…
A new mathematical model for non-equilibrium evaporation/condensation including boiling effect is proposed. A simplified differential-algebraic system of equations is obtained. A code to solve numerically this differential-algebraic system…
We propose a field-theoretical approach to a polymer system immersed in an ideal mixture of clustering centers. The system contains several species of these clustering centers with different functionality, each of which connects a fixed…
Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NpT) ensembles. In their simplest application, a biological system of interest is…
We consider three different continuum polymer models, that all depend on a tunable parameter r that determines the strength of the excluded-volume interactions. In the first model chains are obtained by concatenating hard spherocylinders of…
Introducing nanorods into a polymeric matrix can enhance the physical and mechanical properties of the resulting material. In this paper, we focus on understanding the dispersion and orientation patterns of nanorods in an unentangled…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Phase diagrams serve as a highly informative tool for materials design, encapsulating information about the phases that a material can manifest under specific conditions. In this work, we develop a method in which Bayesian inference is…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…