Related papers: Non-random coil behavior as a consequence of exten…
The rheology of dense amorphous materials under large shear strain is not fully understood, partly due to the difficulty of directly viewing the microscopic details of such materials. We use a colloidal suspension to simulate amorphous…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
A bonded particle model is used to explore how variations in the material properties of brittle, isotropic solids affect critical behavior in fragmentation. To control material properties, a new model is proposed which includes breakable…
Emerging coherent X-ray scattering patterns of single particles have shown dominant morphological signatures in agreement with predictions of the scattering model used for conventional protein crystallography. The key question is if and to…
We show that gels formed by arrested spinodal decomposition of protein solutions exhibit elastic properties in two distinct frequency domains, both elastic moduli exhibiting a remarkably strong dependence on volume fraction. Considering the…
We use confocal microscopy and time-resolved light scattering to investigate plasticity in a col- loidal polycrystal, following the evolution of the network of grain boundaries as the sample is submitted to thousands of shear deformation…
While the physics of disordered packing in non-growing systems is well understood, unexplored phenomena can emerge when packing takes place in growing domains. We study the arrangements of pigment cells (chromatophores) on squid skin as a…
Micron-scale single crystalline materials deform plastically via large intermittent strain bursts that make the deformation process unpredictable. Here we investigate this stochastic phenomenon by analysing the plastic response of an…
Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and…
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
Patterns are quotidian in nature. Distinct multiscale patterns are generally a consequence of nonequilibrium dynamical processes associated with mechanical or hydrodynamic instabilities. In this thesis, I report experimental investigations…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
Unfolding of a coarse grained COVN protein from its native configuration shows a linear response with increasing temperature followed by a nonmonotonic double peaks in its radius of gyration. The protein conforms to a random coil of folded…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino acids $f_{\rm core}$, packing fraction $\langle \phi\rangle$ of…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…