Related papers: Extracting folding landscape characteristics of bi…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
We derive a general expression for electric and magnetic part of the near-field energy density of $N$ dipoles of temperatures $T_1, \ldots, T_N$ immersed in a background field having a different temperature $T_b$. In contrast to former…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
A microscopic understanding of low-temperature thermodynamics and its relation to dynamical features such as a fragile-to-strong crossover (FSC) remains a central challenge in glass physics. Using swap Monte Carlo combined with a full…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
A method is presented that, when used in conjunction with single molecule experimental techniques, allows for the extraction of rates and mechanical properties of a biomolecule undergoing transitions between mechanically distinct states.…
The thermodynamic and kinetic anomalies of supercooled liquids are analyzed from the perspective of energy landscapes. A mean field model, a generalized random energy model of liquids is developed, which exhibits a dynamical transition of…
Dynamic force spectroscopy of single molecules is described by a model which predicts a distribution of rupture forces, the corresponding mean rupture force and variance, all amenable to experimental tests. The distribution has a pronounced…
Energy-Based Models (EBMs) have proven to be a highly effective approach for modelling densities on finite-dimensional spaces. Their ability to incorporate domain-specific choices and constraints into the structure of the model through…
Calculations of electronic and optical properties of solids at finite temperature including electron-phonon interactions and quantum zero-point renormalization have enjoyed considerable progress during the past few years. Among the emerging…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
We have performed power spectral analysis of surface temperatures, velocities, and magnetic fields, using spectro-polarimetric data taken with the Hinode Solar Optical Telescope. When we make power spectra in a field-of-view covering the…
By means of molecular dynamics simulations, we study the stationary points of the potential energy in a Lennard-Jones liquid, giving a purely geometric characterization of the energy landscape of the system. We find a linear relation…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics…