相关论文: Derivation of the Invariant Free-Energy Landscape …
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
The free energy principle (FEP) states that any dynamical system can be interpreted as performing Bayesian inference upon its surrounding environment. In this work, we examine in depth the assumptions required to derive the FEP in the…
A novel energy landscape model, ELM, for proteins recently explained a collection of incoherent, elastic neutron scattering data from proteins. The ELM of proteins considers the elastic response of the proton and its environment to the…
We address the problem of constructing accurate mathematical models of the dynamics of complex systems projected on a collective variable. To this aim we introduce a conceptually simple yet effective algorithm for estimating the parameters…
The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
It is difficult to relate the properties of liquids and glasses directly to their structure because of complexity in the structure which defies precise definition. The potential energy landscape (PEL) approach is a very insightful way to…
The dynamics of unimolecular photo-triggered reactions can be strongly affected by the surrounding medium. An accurate description of these reactions requires knowing the free energy surface (FES) and the friction felt by the reactants.…
Given nonstationary data from molecular dynamics simulations, a Markovian Langevin model is constructed that aims to reproduce the time evolution of the underlying process. While at equilibrium the free energy landscape is sampled,…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
We extend the energetic variational approach so it can be applied to a chemical reaction system with general mass action kinetics. Our approach starts with an energy-dissipation law. We show that the chemical equilibrium is determined by…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
The use of effective field theory offers a systematic way to improve calculations of nuclear reactions and the properties of atomic nuclei. Its successes have led to the widespread belief that the predictions of this approach are model…
We propose a new model for description of electrons beam dynamics in Free Electron Laser (FEL) undulator, based on the method of linear time-dependent invariants of quantum-mechanical charge particle. The magnetic field has periodic…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
A new three dimensional model of the FEL is presented. A system of scaled, coupled Maxwell Lorentz equations are derived in the paraxial limit. A minimal number of limiting assumptions are made and the equations are not averaged in the…
For decades, it was unknown how electron bifurcating systems in Nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron bifurcating molecular machines could not be designed and built.…
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram…