Related papers: Optimized Baxter Model of Protein Solutions: Elect…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
A new statistical mechanics formulation of characterizing the structural fluctuation of protein correlated with that of water is presented based on the generalized Langevin equation and the 3D-RISM/RISM theory of molecular liquids. The…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
It has recently been shown that a free energy for Baxter's sticky hard sphere fluid is uniquely defined within the framework of fundamental measure theory (FMT) for the inhomogeneous hard sphere fluid, provided that it obeys scaled-particle…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying…
A statistical theory is presented of the magnesium ion interacting with lysozyme under conditions where the latter is positively charged. Temporarily assuming magnesium is not noncovalently bound to the protein, I solve the nonlinear…
We developed a lattice dynamical theory of an atomically-thin compressional piezoelectric resonator. Acoustic and optical dynamic displacement response functions are derived and account for frequency-dependent electromechanical coupling.…
The equilibrium state of a system consisting of a large number of strongly interacting electrons can be characterized by its density operator. This gives a direct access to the ground-state energy or, at finite temperatures, to the free…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
We present a general energy approach to study the unsteady adhesive contact of viscoelastic materials. Under the assumption of infinitely short-range adhesive interactions, we exploit the principle of virtual work to generalize Griffith…
The structure of the Baxter adhesive hard sphere fluid is examined using computer simulation. The radial distribution function (which exhibits unusual discontinuities due to the particle adhesion) and static structure factor are calculated…
Small angle neutron scattering intensity distributions taken from cytochrome C and lysozyme protein solutions show a rising intensity at very small wave vector, Q, which can be interpreted in terms of the presence of a weak long-range…
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…
An improved linear model is developed for elasto-plastic and adhesive contact. New correlations are proposed and validated to estimate the key input parameters of the model, including contact stiffness, yield point, maximum pull-off force…
We present a general expression for the association rate for partially diffusion-controlled reactions between spherical molecules with an asymmetric reactive patch on each surface. Reaction can occur only if the two patches are in contact…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…