Related papers: Evolution and Mutations of Beta 2 Microglobulin
Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…
We investigate through high resolution 3D simulations the nonlinear evolution of compressible magnetohydrodynamic flows subject to the Kelvin-Helmholtz instability. We confirm in 3D flows the conclusion from our 2D work that even apparently…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
Sub-Neptunes occupy an intriguing region of planetary mass-radius space, where theoretical models of interior structure predict that they could be water-rich, where water is in steam and supercritical state. Such planets are expected to…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
Metamorphic proteins like Lymphotactin are a notable exception of the empirical principle that structured natural proteins possess a unique three dimensional structure. In particular, the human chemokine lymphotactin protein (Ltn) exists in…
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations…
The evolution of mesoscopic structure for cement-water mixtures turning into colloidal gels remains far from being understood. Recent neutron scattering investigations (Phys. Rev. Lett. 93, 255704 (2004); Phys. Rev. B. 72, 224208 (2005);…
While modern structural biology has provided us with a rich and diverse picture of membrane proteins, the biological function of membrane proteins is often influenced by the mechanical properties of the surrounding lipid bilayer. Here we…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions…
The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is…
A hydrodynamic model is proposed to describe one of the most critical problems in intensive medical care units: the formation of biofilms inside central venous catheters. The incorporation of approximate solutions for the flow-limited…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
The design and development of inexpensive highly efficient electrocatalysts for hydrogen production, underpins several emerging clean-energy technologies. In this work, for the first time, molybdenum disulfide (MoS2) nanodots have been…
Transitions between metabasins in supercooled liquids seem to occur through rapid "democratic" collective particle rearrangements. Here we show that this apparent homogeneous particle motion is a direct consequence of dynamic facilitation.…
The hydrodynamic processes operating within stellar interiors are far richer than represented by the best stellar evolution model available. Although it is now widely understood, through astrophysical simulation and relevant terrestrial…
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from…