Related papers: Disordered peptide chains in an {\alpha}-C-based c…
Three fundamental segregation and pattern formation processes are known in granular mixtures in a rotating cylindrical drum: radial segregation, axial banding, and coarsening of the band pattern. While the mechanism for the first effect is…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
In this paper we use a formal discrete-to-continuum procedure to derive a continuum variational model for two chains of atoms with slightly incommensurate lattices. The chains represent a cross-section of a three-dimensional system…
The large time and length scales and, not least, the vast number of particles involved in industrial-scale simulations inflate the computational costs of the Discrete Element Method (DEM) excessively. Coarse grain models can help to lower…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
The enormous size and complexity of genotypic sequence space frequently requires consideration of coarse-grained sequences in empirical models. We develop scaling relations to quantify the effect of this coarse-graining on properties of…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
The primary structures of peptides, originating from food proteins, affect their taste. Connecting primary structure to taste, however, is difficult because the size of the peptide sequence space increases exponentially with increasing…
We investigate one dimensional tight binding model in the presence of a correlated binary disorder. The disorder is due to the interaction of particles with heavy immobile other species. Off-diagonal disorder is created by means of a fast…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
We investigate transport properties of topologically disordered, three-dimensional, one-particle, tight binding models, featuring site distance dependent hopping terms. We start from entirely disordered systems into which we gradually…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
The human proteome is enriched in proteins that do not fold into a stable 3D structure. These intrinsically disordered proteins (IDPs) spontaneously fluctuate between a large number of configurations in their native form. Remarkably, the…
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
Conformational properties of intrinsically disordered proteins (IDPs) are governed by a sequence-ensemble relationship. To differentiate the impact of sequence-local versus sequence-nonlocal features of an IDP's charge pattern on its…
We consider two particles hopping on a chain with a contact interaction between them. At strong interaction, there is a molecular bound state separated by a direct gap from a continuous band of atomic states. Introducing weak disorder in…