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A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
Understanding how biological constraints shape neural computation is a central goal of computational neuroscience. Spatially embedded recurrent neural networks provide a promising avenue to study how modelled constraints shape the combined…
Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…
Objectives: Functional connectivity triggered by naturalistic stimulus (e.g., movies) and machine learning techniques provide a great insight in exploring the brain functions such as fluid intelligence. However, functional connectivity are…
We study the elasticity of a two-dimensional random network of rigid rods (``Mikado model''). The essential features incorporated into the model are the anisotropic elasticity of the rods and the random geometry of the network. We show that…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Protein function prediction is dominated by representations grounded in sequence and static structure, neither of which captures the collective vibrational dynamics through which proteins act. Here we introduce frequency-space mechanics, a…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
The elastic response is studied of a single flexible chain grafted on a rigid plane and an ensemble of non-interacting tethered chains. It is demonstrated that the entropic theory of rubber elasticity leads to conclusions that disagree with…
Viscosity, the resistance of a liquid to flow, is driven by atomic-scale friction but its microscopic origin remains poorly understood. We use a theoretical framework based on nonaffine linear response to decompose the viscosity of metallic…
A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
Running is a fundamental form of human locomotion and a key task for evaluating neuromuscular control and lower-limb coordination. In recent years, muscle synergy analysis based on surface electromyography (sEMG) has become an important…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Many biological tissues feature a heterogeneous network of fibers whose tensile and bending rigidity contribute substantially to these tissues' elastic properties. Rigidity percolation has emerged as a important paradigm for relating these…
Predicting the macroscopic mechanical behavior of polymeric materials from the micro-structural features has remained a challenge for decades. Existing theoretical models often fail to accurately capture the experimental data, due to…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…