Related papers: Computing and Bounding Equilibrium Concentrations …
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…
This paper presents a thermodynamically consistent model for multicomponent electrolyte solutions. The first part of this paper derives the general governing equations for nonequilibrium systems within the theory of nonequilibrium…
We present simulations on a binary blend of bead-spring polymer chains. The introduction of monomer size disparity yields very different relaxation times for each component of the blend. Competition between two different arrest mechanisms,…
Two-dimensional ionic liquids with single site anion and cation-neutral dimer are studied by computer simulations and integral equation techniques, with the aim of characterizing differences with single site anion-cation mixtures, and also…
By molecular dynamics simulations and free energy calculations based on Monte Carlo method, the detailed balance between Pt cluster isomers was investigated. For clusters of n<=50, stationary equilibrium is achieved in 100 ns in the…
The discovery of complex concentrated alloys has unveiled materials with diverse atomic environments, prompting the exploration of solute segregation beyond dilute alloys. Data-driven methods offer promising for modeling segregation in such…
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated…
Living systems produce "persistent" copies of information-carrying polymers, in which template and copy sequences remain correlated after physically decoupling. We identify a general measure of the thermodynamic efficiency with which these…
We consider viscous, heat conducting mixtures of molecularly miscible chemical species forming a fluid in which the constituents can undergo chemical reactions. Assuming a common temperature for all components, we derive a closed system of…
We introduce an approach for the accurate calculation of thermal properties of classical nanoclusters. Based on a recently developed enhanced sampling technique, replica exchange metadynamics, the method yields the true free energy of each…
For open quantum systems coupled to a thermal bath at inverse temperature $\beta$, it is well known that under the Born-, Markov-, and secular approximations the system density matrix will approach the thermal Gibbs state with the bath…
A novel approach is presented for the solution of instantaneous chemical equilibrium problems. The chemical equilibrium can be considered, due to its intrinsically local character, as a mapping of the three-dimensional parameter space…
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…
Directed polymers on 1+1 dimensional lattices coupled to a heat bath at temperature $T$ are studied numerically for three ensembles of the site disorder. In particular correlations of the disorder as well as fractal patterning are…
From the crystal structure data and using the concept of equilbrium statistical mechanics we show how to calculate the thermodynamics of protein/DNA complexes. We apply the method to the TATA-box binding protein (TBP)/TATA sequence complex.…
A coarse-grained multi-blob description of polymer solutions is presented, based on soft, transferable effective interactions between bonded and non-bonded blobs. The number of blobs is chosen such that the blob density does not exceed…
The classical bond-fluctuation model (BFM) is an efficient lattice Monte Carlo algorithm for coarse-grained polymer chains where each monomer occupies exclusively a certain number of lattice sites. In this paper we propose a generalization…
In silico design of new molecules and materials with desirable quantum properties by high-throughput screening is a major challenge due to the high dimensionality of chemical space. To facilitate its navigation, we present a unification of…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branched model polymers, or `colloidomers'. The distribution of…