Related papers: Molecular Dynamics Studies on the Buffalo Prion Pr…
Charge transport in organic semiconductors is limited by dynamical disorder. Design rules for new high-mobility materials have therefore focused on limiting its two foundations: structural fluctuations and the transfer integral gradient.…
The use of beta-solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their…
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
Molecular chaperones play a prominent role in signaling and transcriptional regulatory networks of the cell. Recent advances uncovered that chaperones act as genetic buffers stabilizing the phenotype of various cells and organisms and may…
We study the correlation between the codon usage bias of genetic sequences and the network features of protein-protein interaction (PPI) in bacterial species. We use PCA techniques in the space of codon bias indices to show that genes with…
We describe Structured Random Binding (SRB), a minimal model of protein-protein interactions rooted in the statistical physics of disordered systems. In this model, nonspecific binding is a generic consequence of the interaction between…
Solar water splitting has received a lot of attention due to its high efficiency and clean energy production potential. Herein, based on the band alignment principle, the g-C3N4/TiO2-B(001) heterostructure is strategically designed, then a…
The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Prior work focused on supervised learning methods using a large set of binding affinity data for small molecules, but it is hard to apply the same…
The migration of grain boundaries leads to grain growth in polycrystals and is one mechanism of grain-boundary-mediated plasticity, especially in nanocrystalline metals. This migration is due to the movement of dislocation-like defects,…
The migration of grain boundaries leads to grain growth in polycrystals and is one mechanism of grain-boundary-mediated plasticity, especially in nanocrystalline metals. This migration is due to the movement of dislocation-like defects,…
BaBiO$_3$ is a mixed-valence perovskite which escapes the metallic state through a Bi valence (and Bi-O bond) disproportionation or CDW distortion, resulting in a semiconductor with a gap of 0.8 eV at zero pressure. The evolution of…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
In this paper we study the phenomenon of kinetic partitioning when a polypeptide chain has two ground state conformations one of which is more kinetically reachable than the other. This question is relevant to understand the phenomenology…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
Predicting the binding affinity of protein protein complexes directly from sequence remains a challenging problem, particularly in the absence of reliable structural information. Here I present ProtT Affinity, a sequence only model that…