Related papers: New method for deciphering free energy landscape o…
The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
A melting transition for a system of hard spheres interacting by a repulsive Yukawa potential of DLVO form is studied. To find the location of the phase boundary, we propose a simple theory to calculate the free energies for the coexisting…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
Simulated sliding between an oxidized silicon tip and surface over six decades of velocity using accelerated molecular dynamics reproduces the experimentally observed velocity dependence of the friction force. Unlike in the crystalline…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
We investigate the mechanism of chain exchange in diblock copolymer micelles using two distinct yet complementary simulation techniques. First, enhanced sampling method is combined with coarse-grained molecular dynamics to compute a…
We present a method for determining the free energy of coexisting states from irreversible work measurements. Our approach is based on a fluctuation relation that is valid for dissipative transformations in partially equilibrated systems.…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Experiments show that for many two state folders the free energy of the native state DG_ND([C]) changes linearly as the denaturant concentration [C] is varied. The slope, m = d DG_ND([C])/d[C], is nearly constant. The m-value is associated…
We introduce a computational framework for generating realistic transition paths between distinct conformations of large bio-molecular systems. The method is built on a stochastic integro-differential formulation derived from the Langevin…
When particles/molecules diffuse in systems that contain obstacles, the steady-state regime (during which the mean-square displacement scales linearly with time, $\left< r^2 \right> \sim t$) is preceded by a transient regime. It is common…
Understanding the transition events between metastable states in complex systems is an important subject in the fields of computational physics, chemistry and biology. The transition pathway plays an important role in characterizing the…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
Let Delta F be the free energy difference between two equilibrium states of a system. An established method of numerically computing Delta F involves a single, long ``switching simulation'', during which the system is driven reversibly from…