Related papers: Multiple Folding Pathways of the SH3 domain
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that DeltaT/T_F ~ N^-1, where T_F is the folding transition…
Two ferromagnetic phases, FM1 and FM2, were first proposed to exist in LaCrGe$_3$ based on a broad maximum in the temperature derivative of resistivity resembling that of the superconducting ferromagnet UGe$_2$ where FM1 and FM2 are…
We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We…
Molecular dynamics simulations of SPC/E water confined in a Silica pore are presented. The simulations have been performed at different hydration levels and temperatures to study the single-particle dynamics. Due to the confinement and to…
The photoinduced switching of Fe(II)-based spin-crossover complexes from singlet to quintet takes place at ultrafast time scales. This a priori spin-forbidden transition triggered numerous time-resolved experiments of solvated samples to…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
Although known that single domain proteins fold and unfold by parallel pathways, demonstration of this expectation has been difficult to establish in experiments. Unfolding rate, $k_\mathrm{u}(f)$, as a function of force $f$, obtained in…
Voltage gated channel proteins cooperate in the transmission of membrane potentials between nerve cells. With the recent progress in atomic-scaled biological chemistry it has now become established that these channel proteins provide highly…
We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…
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 study the transport properties of a one-dimensional spinful Fermi gas, after junction of two semi-infinite sub-systems held at different temperatures. The ensuing dynamics is studied by analysing the space-time profiles of local…
Ternary flavor mixtures of ultracold fermionic atoms in an optical lattice are studied in the case of equal, repulsive on-site interactions U>0. The corresponding SU(3) invariant Hubbard model is solved numerically exactly within dynamical…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
We study a spin system with two- and four-spin exchange interactions on the triangular lattice, which is a possible model for the nuclear magnetism of solid $^3$He layers. It is found that a novel spin structure with scalar chiral order…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
The experimental calorimetric two-state criterion requires the van't Hoff enthalpy $\Delta H_{\rm vH}$ around the folding/unfolding transition midpoint to be equal or very close to the calorimetric enthalpy $\Delta H_{\rm cal}$ of the…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…