相关论文: Free Energy Evaluation in Polymer Translocation vi…
Most non-equilibrium processes in thermodynamics are quantified only by inequalities, however the Jarzynski relation presents a remarkably simple and general equality relating non-equilibrium quantities with the equilibrium free energy, and…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
Applying the method from recently developed fluctuation theorems to the stochastic dynamics of single macromolecules in ambient fluid at constant temperature, we establish two Jarzynski-type equalities: (1) between the log-mean-exponential…
We consider the escape of a flexible, self-avoiding polymer chain out of a confined geometry. By means of simulations, we demonstrate that the translocation time can be described by a simple scaling law that exhibits a nonlinear dependence…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
The Jarzynski equality relates the free energy difference between two equilibrium states to the fluctuating irreversible work afforded to switch between them. The prescribed fixed temperature for the equilibrium states implicitly constrains…
We investigate the role of fluctuations in single molecule measurements of torque-link ($t-lk$) curves. For semiflexible polymers of finite persistence length (i.e. polymers with contour length $L$ comparable to the persistence length…
In thermodynamically characterizing a mixture comprising a finite number of molecules, we consider two kinds of protocol for producing a mixture from a pure substance. The first is a single alchemical operation, whereas the second is a…
We present a Generalized Langevin Equation for the dynamics of interacting semiflexible polymer chains, undergoing slow cooperative dynamics. The calculated Gaussian intermolecular center-of-mass and monomer potentials, wich enter the GLE,…
We use lattice-Boltzmann molecular dynamics (LBMD) simulations to study the compression of a confined polymer immersed in a fluid and pushed by a large spherical colloid with a diameter comparable to the channel width. We examined the…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
Using a model-independent low-energy effective field theory, we calculate the free energy of three-dimensional antiferromagnets in a combination of mutually perpendicular external magnetic and staggered fields at the…
We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of…
We consider a long, semiflexible polymer, with persistence length $P$ and contour length $L$, fluctuating in a narrow cylindrical channel of diameter $D$. In the regime $D\ll P\ll L$ the free energy of confinement $\Delta F$ and the length…
In this paper, we report dynamic Monte Carlo simulations of melting and crystallization in a single-chain system. Their free energy barriers are calculated by the umbrella sampling method and can be described well by a simple expression…
We consider two configurations of a random directed polymer of length L confined to a plane and ending in two points separated by 2u. Defining the mean free energy $\bar F$ and the free energy difference F' of the two configurations, we…
We study the ternary Ohta-Kawasaki free energy that has been used to model triblock copolymer systems. Its one-dimensional global minimizers are conjectured to have cyclic patterns. However, some physical experiments and computer…
In this paper, we study the free energy of the directed polymer on a cylinder of radius $L$ with the inverse temperature $\beta$. Assuming the random environment is given by a Gaussian process that is white in time and smooth in space, with…
Three-dimensional quantum electrodynamics exhibits a number of interesting properties, such as dynamical chiral symmetry breaking, weak confinement, and non-Fermi liquid behavior, and also has wide applications in condensed matter physics.…
Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although, complex functionalities often emerge from the simultaneous interaction of…