Related papers: Energy landscape theory for cotranslational protei…
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…
Perturbing a Go model towards a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
Absorption of elastic waves in complex media is commonly found to increase linearly with frequency, for both longitudinal and shear waves. This ubiquitous property is observed in media such as rocks, unconsolidated sediments, and human…
The potential energy landscape, PEL, theory stands as one of the most successful frameworks for understanding supercooled liquids and glassy systems. A central element of this theory is the configurational entropy, Sc, which is…
To celebrate Hans Frauenfelder's achievements, we examine energy(-like) "landscapes" for complex living systems. Energy landscapes summarize all possible dynamics of some physical systems. Energy(-like) landscapes can explain some…
Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function.…
Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale that is inaccessible to conventional simulations. Despite…
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…
Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery.…
We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors…
In many statistical learning problems, the target functions to be optimized are highly non-convex in various model spaces and thus are difficult to analyze. In this paper, we compute \emph{Energy Landscape Maps} (ELMs) which characterize…
Rugged energy landscapes find wide applications in diverse fields ranging from astrophysics to protein folding. We study the dependence of diffusion coefficient $(D)$ of a Brownian particle on the distribution width $(\varepsilon)$ of…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
Major efforts in recent years have been directed towards understanding molecular transport in polymeric membranes, in particular reverse osmosis and nanofiltration membranes. Transition-state theory is an increasingly common approach to…
Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…