Related papers: Protein structural variation in computational mode…

We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the…

We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three…

Using a new semi empirical method for calculating molecular polarizabilities and the Clausius Mossotti relation, we calculated the static dielectric constants of dry proteins for all structures in the protein data bank (PDB). The mean…

In this article we explore how structural parameters of composites filled with one-dimensional, electrically conducting elements (such as sticks, needles, chains, or rods) affect the percolation properties of the system. To this end, we…

We use molecular dynamics to study the ordering of a nematic liquid crystal around a spherical particle or droplet. Homeotropic boundary conditions and strong anchoring create a hedgehog director configuration on the particle surface and in…

We present a new method to extract distance and orientation dependent potentials between amino acid side chains using a database of protein structures and the standard Boltzmann device. The importance of orientation dependent interactions…

Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…

Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…

Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…

We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…

The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…

First-principles based modeling on phonon dynamics and transport using density functional theory and Boltzmann transport equation has proven powerful in predicting thermal conductivity of crystalline materials, but it remains unfeasible for…

Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…

Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…

Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational…

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…

Due to the highly complex chemical structure of biomolecules, the extensive understanding of the electronic information for proteomics can be challenging. Here, we constructed a charge transfer database at residue level derived from…

Fifteen years ago Monique Tirion showed that the low-frequency normal modes of a protein are not significantly altered when non-bonded interactions are replaced by Hookean springs, for all atom pairs whose distance is smaller than a given…

Amorphous solids tend to present an abundance of soft elastic modes, which diminish their transport properties, generate heterogeneities in their elastic response, and affect non-linear processes like thermal activation of plasticity. This…

Recent developments in deep learning-based methods demonstrated its potential to predict the 3D protein structures using inputs such as protein sequences, Cryo-Electron microscopy (Cryo-EM) images of proteins, etc. However, these methods…