Related papers: Selection originating from protein foldability: I.…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
Stochastic thermodynamics is formulated under the assumption of perfect knowledge of all thermodynamic parameters. However, in any real-world experiment, there is non-zero uncertainty about the precise value of temperatures, chemical…
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
When exposed to a thermal gradient, reaction networks can convert thermal energy into the chemical selection of states that would be unfavourable at equilibrium. The kinetics of reaction paths, and thus how fast they dissipate available…
Polymers near the glass transition temperature Tg often exhibit a breakdown of time-temperature-superposition (TTS), with chain relaxation times and viscosity exhibiting a weaker temperature dependence than segmental relaxation times. The…
We investigated the atomic fill site probability distributions across supercell structures of RT12-xTi (R=Nd, Sm, T=Fe, Co). We use a combined molecular dynamics and Boltzmann distribution approach to extrapolate the probability…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by softening of the vibrational force constant by electrostatic and van der Waals forces…
A single mechanism, endemic to the standard model of physics, is proposed to explain wavefunction collapse, classical motion, dissipation, equilibration, and the transition from pure quantum mechanics through open system decoherence to the…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
A thermodynamic system of non-interacting quantum particles changes its statistical distribution formulas if there is a universal limitation for the size of energetic quantum leaps (magnitude of quantum leaps smaller than Planck energy). By…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
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…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
We compute the full probability distribution of the moment of inertia $I \propto \sum_{i=1}^N \vec{r}_i^{\,2}$ of a gas of $N$ noninteracting bosons trapped in a harmonic potential $V(r) = (1/2)\, m\, \omega^2 r^2$, in all dimensions and at…
Boltzmann's principle is used to select the "most probable" realization (macrostate) of an isolated or closed thermodynamic system, containing a small number of particles ($N \llsp \infty$), for both classical and quantum statistics. The…
We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…