Energy landscape and rigidity

Rigidity and Energy

Suppose one holds two sticks in the form of a cross in one hand, and places a rubber band in tension around the four ends. When it is released, it comes to rest in the shape of a convex quadrilateral in a plane. It always returns to the same shape, no matter how it is distorted, as long as the ends do not slip, and the rubber band does not break. This is a very simple example of a "rigid" frame...

transitions - energy landscape distinctions

Protein energy landscape roughness.

The 'new view' of proteins sees protein reactions as parallel processes occurring along funnelled energy landscapes. These landscapes are generally not smooth, but are superimposed by hills and valleys of different heights and widths leading to roughness on the energy surface. In the present paper, we describe the origins of protein energy landscape roughness, measurements of its scale and its ...

Certifying the Potential Energy Landscape

It is highly desirable for numerical approximations to stationary points for a potential energy landscape to lie in the corresponding quadratic convergence basin. However, it is possible that an approximation may lie only in the linear convergence basin, or even in a chaotic region, and hence not converge to the actual stationary point when further optimization is attempted. Proving that a nume...

Energy landscape in protein folding and unfolding.

We use (1)H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295 < T < 365 K and following different trajectories along the protein e...