相关论文: Thermally activated processes in polymer dynamics
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
The collective behavior of thermally active structures offers clues on the emergent degrees of freedom and the physical mechanisms that determine the low energy state of a variety of systems. Here, the thermally active dynamics of magnetic…
The conformational and dynamical properties of isolated semiflexible active polar ring polymers are investigated analytically. A ring is modeled as continuous Gaussian polymer exposed to tangential active forces. The analytical solution of…
Every time a chemical reaction occurs, an energy exchange between reactants and environment exists, which is defined as the enthalpy of the reaction. In the last decades, research has resulted in an increasing number of devices at the…
The behavior of a particle in a solvent has been framed using stochastic dynamics since the early theory of Kramers. A particle in a chemical reaction reacts slower in a diluted solvent because of the lack of energy transfer via collisions.…
We calculate thermodynamic quantities of HP lattice proteins by means of a multicanonical chain growth algorithm that connects the new variants of the Pruned-Enriched Rosenbluth Method (nPERM) and flat histogram sampling of the entire…
Jamming is a common feature of out of equilibrium systems showing slow relaxation dynamics. Here we review our efforts in understanding jamming in granular materials using experiments and computer simulations. We first obtain an estimation…
The freely jointed chain is often applied to model the thermodynamics of single polymer chains, but the traditional formulation of the model lacks internal energy changes due to bond stretching. For this reason, the extensible freely…
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent…
We develop a non-empirical scheme to search for the minimum-energy escape paths from the minima of the potential surface to unknown saddle points nearby. A stochastic algorithm is constructed to move the walkers up the surface through the…
Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of…
We propose a way to analyze the landscape geometry explored by a glassy system after a quench solely based on time series of energy values recorded during a simulation. Entry and exit times for landscape `valleys' are defined operationally…
An approach for analytical description of thermal processes in harmonic lattices is presented. We cover longitudinal and transverse vibrations of chains and out-of-plane vibrations of two-dimensional lattices with interactions of an…
In this paper we view the steady states of classical random walks over complex networks with an arbitrary degree distribution as states in thermal equilibrium. By identifying the distribution of states as a canonical ensemble, we are able…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
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 extension of thermodynamic principles to active matter remains a challenge due to the non-equilibrium nature inherent to active systems. In this study, we introduce a framework to assess entropy in our minimal macroscopic experiment…
The interplay of topological constraints, excluded volume interactions, persistence length and dynamical entanglement length in solutions and melts of linear chains and ring polymers is investigated by means of kinetic Monte Carlo…
We present a novel path-integral method for the determination of time-dependent and time-averaged reaction rates in multidimensional, periodically driven escape problems at weak thermal noise. The so obtained general expressions are…