Related papers: New method for deciphering free energy landscape o…
We study the thermodynamical properties of a topology-based model proposed by Galzitskaya and Finkelstein for the description of protein folding. We devise and test three different mean-field approaches for the model, that simplify the…
We introduce an approach for performing "very long" computer simulations of the dynamics of simplified, folded proteins. Using an alpha-carbon protein model and a fine grid to mimic continuum computations at increased speed, we perform…
We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three dimensional space. Our approach is based on the concept of an intrinsically discrete curve, which enables us to more effectively…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized,…
We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We obtain…
We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described…
Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…
We present a differentiable soft-body physics simulator that can be composed with neural networks as a differentiable layer. In contrast to other differentiable physics approaches that use explicit forward models to define state…
The overall structure of the transition state and intermediate ensembles experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can be obtained utilizing simplified models which have almost no energetic frustration. The…
The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
We propose that the pseudogap state observed in the transition metal oxides can be explained by a three-dimensional flux state, which exhibits spontaneously generated currents in its ground state due to electron-electron correlations. We…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
We propose an energy-stable parametric finite element method (ES-PFEM) for simulating solid-state dewetting of thin films in two dimensions via a sharp-interface model, which is governed by surface diffusion and contact line (point)…
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…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
A phase-field model that allows for quantitative simulations of low-speed eutectic and peritectic solidification under typical experimental conditions is developed. Its cornerstone is a smooth free-energy functional, designed so that the…
We describe a robust and efficient chain-of-states method for computing Minimum Energy Paths~(MEPs) associated to barrier-crossing events in poly-atomic systems. The path is parametrized in terms of a continuous variable $t \in [0,1]$ that…
A formalism is developed to study certain five-term recursion relations by discrete phase integral (or Wentzel-Kramers-Brillouin) methods. Such recursion relations arise naturally in the study of the Schrodinger equation for certain spin…