Surveying the free energy landscapes of continuum models: Application to soft matter systems.
نویسنده
چکیده
A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods allow systematic study of not only the most relevant minimum energy configurations, but also the transition pathways between any two minima, as well as their corresponding energy barriers and transition state configurations. A global view of the free energy landscapes can then be visualized using either a disconnectivity graph or a network representation. Different forms of free energy functionals and boundary conditions can be readily implemented, thus allowing these tools to be utilised for a broad range of problems.
منابع مشابه
Hidden structure in protein energy landscapes.
Inherent structure theory is used to discover strong connections between simple characteristics of protein structure and the energy landscape of a Gō model. The potential energies and vibrational free energies of inherent structures are highly correlated, and both reflect simple measures of networks of native contacts. These connections have important consequences for models of protein dynamics...
متن کاملDirect evidence of the multidimensionality of the free-energy landscapes of proteins revealed by mechanical probes.
The study of mechanical unfolding, through the combined efforts of atomic force microscopy and simulation, is yielding fresh insights into the free-energy landscapes of proteins. Thus far, experiments have been mostly analyzed with one-dimensional models of the free-energy landscape. We show that as the two ends of a protein, filamin, are pulled apart at a speed tending to zero, the measured me...
متن کاملApplication of Nano-Contact Mechanics Models in Manipulation of Biological Nano-Particle: FE Simulation
Contact mechanics is related to the deformation study of solids that meet each other at one or more points. The physical and mathematical formulation of the problem is established upon the mechanics of materials and continuum mechanics and focuses on computations involving bodies with different characteristics in static or dynamic contact. Contact mechanics gives essential information for the s...
متن کاملTransport and fractionation in periodic potential-energy landscapes.
Objects driven through periodically modulated potential-energy landscapes in two dimensions can become locked in to symmetry-selected directions that are independent of the driving force's orientation. We investigate this problem in the overdamped limit, and demonstrate that the crossover from free-flowing to locked-in transport can depend exponentially on an object's size, with this exceptiona...
متن کاملVelocity convergence of free energy surfaces from single-molecule measurements using Jarzynski's equality.
We studied the velocity dependence of mechanical unfolding of single protein molecules with the atomic force microscope. We showed that with enough realizations, the free energy surfaces reconstructed from Jarzynski's equality converge with respect to pulling velocity, in good agreement with theory. Using the I27 domain of titin as an example, we estimated the required number of realizations fo...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- The Journal of chemical physics
دوره 142 12 شماره
صفحات -
تاریخ انتشار 2015