Related papers: Vibrational entropy and the structural organizatio…
Motivation: Profile hidden Markov Models (pHMMs) are a popular and very useful tool in the detection of the remote homologue protein families. Unfortunately, their performance is not always satisfactory when proteins are in the 'twilight…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
Living systems are hierarchical control systems that display a small world network structure, in which many smaller clusters are nested within fewer larger ones, producing a fractal-like structure with a power-law cluster size distribution…
Coupled oscillator networks show a complex interrelations between topological characteristics of the network and the nonlinear stability of single nodes with respect to large but realistic perturbations. We extend previous results on these…
Heterogeneous materials are often organized in a hierarchical manner, where a basic unit is repeated over multiple scales.The structure then acquires a self-similar pattern. Examples of such structure are found in various biological and…
We describe the collective behavior of a system of many inelastic spherical particles inside a box which is being periodically vibrated. The box is shallow, with large horizontal dimensions, while the height is less than two particle…
The problem of detecting specific features of microscopic dynamics in the macroscopic behavior of a many-degrees-of-freedom system is investigated by analyzing the position and momentum time series of a heavy impurity embedded in a chain of…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
Vibrational spectra of proteins and topologically disordered solids display a common anomaly at low frequencies, known as Boson peak. We show that such feature in globular proteins can be deciphered in terms of an energy landscape picture,…
Despite vibrational properties being critical for the ab initio prediction of the finite temperature stability and transport properties of solids, their inclusion in ab initio materials repositories has been hindered by expensive…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We introduce the hierarchical compositional network (HCN), a directed generative model able to discover and disentangle, without supervision, the building blocks of a set of binary images. The building blocks are binary features defined…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral…
Activity in coupled systems is often oscillatory, for example, the firing pattern of neuronal populations. Whereas these oscillations have been studied predominantly in local circuits, here we show how the topology of large-scale networks,…
The heterogeneous micromechanical properties of biological tissues have profound implications across diverse medical and engineering domains. However, identifying full-field heterogeneous elastic properties of soft materials using…
Objective: To characterize the irregularity of the spectrum of a signal, spectral entropy is a widely adopted measure. However, such a metric is invariant under any permutation of the estimations of the powers of individual frequency…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…