Related papers: Sub-residue sharpness of protein helix-coil transi…
\gamma-softness in atomic nuclei is investigated in the framework of energy density functionals. By mapping constrained microscopic energy surfaces for a set of representative non-axial medium-heavy and heavy nuclei to a Hamiltonian of the…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
The basic models of helix-coil transitions in biomolecules are introduced. These include phenomenological, zipper (Bragg-Zimm) models of polypeptides, loop-entropy (Poland-Scheraga) and Hamiltonian (Peyrard-Bishop) models of homogeneous DNA…
We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…
Biological systems exhibit marked molecular asymmetry, with proteins based predominantly on L-amino acids and nucleic acids and carbohydrates largely composed of D-sugars. Explanations for homochirality include asymmetric photochemistry,…
2-Higgs Doublet Models (2HDMs) typically need to invoke an ad-hoc discrete symmetry to avoid severe flavor bounds and in addition feature massless neutrinos, thus falling short of naturally complying with existing data. However, when…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…
Noncommutative spectral geometry offers a purely geometric explanation for the standard model of strong and electroweak interactions, including a geometric explanation for the origin of the Higgs field. Within this framework, the…
The problem of establishing out-of-sample bounds for the values of an unkonwn ground-truth function is considered. Kernels and their associated Hilbert spaces are the main formalism employed herein along with an observational model where…
The spatiotemporal oscillation patterns of the proteins MinD and MinE are used by the bacterium E. coli to sense its own geometry. Strikingly, both computer simulations and experiments have recently shown that for the same geometry of the…
A widely-studied model for gels or biopolymeric fibrous materials are networks with central force interactions, such as Hookean springs. Less commonly studied are materials whose mechanics are dominated by non-central force interactions…
In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At…
The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
We study equilibrium configurations of non-Euclidean plates, in which the reference metric is uniaxially periodic. This work is motivated by recent experiments on thin sheets of composite thermally responsive gels [1]. Such sheets bend…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…
The problem of determining the existence of a spectral gap in a lattice quantum spin system was previously shown to be undecidable for one [J. Bausch et al., "Undecidability of the spectral gap in one dimension", Physical Review X 10…
The predominant structural protein in vertebrates is collagen, which plays a key role in extracellular matrix and connective tissue mechanics. Despite its prevalence and physical importance in biology, the mechanical properties of molecular…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
A geometric transition is a continuous path of geometric structures that changes type, meaning that the model geometry, i.e. the homogeneous space on which the structures are modeled, abruptly changes. In order to rigorously study…