Related papers: Developing an unfolding-incorporated coarse-graine…
Wrinkling, creasing and folding are frequent phenomena encountered in biological and man-made bilayers made by thin films bonded to thicker and softer substrates often containing fibers. Paradigmatic examples of the latter are the skin, the…
What can cells gain by using disordered, rather than folded, proteins in the architecture of their skeleton? Disordered proteins take multiple co-existing conformations, and often contain segments which act as random-walk-shaped polymers.…
The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded…
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
Complex flow fields govern the deformation of polymers in various manufacturing processes. However, high flow rates may trigger reaction events (i.e., bond breaking or undesirable reaction of mechanophores) in raw polymeric materials,…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Entangled networks of stiff biopolymers exhibit complex dynamic response, emerging from the topological constraints that neighboring filaments impose upon each other. We propose a class of reference models for entanglement dynamics of stiff…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
Heteropolymers are ubiquitous in both synthetic systems, such as block copolymers, and biological macromolecules, including proteins and nucleic acids. Beyond their chemical composition, these polymers often exhibit spatial variations in…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
This work presents a novel framework governing the development of an efficient, accurate, and transferable coarse-grained (CG) model of a polyether material. The proposed framework combines the two fundamentally different classical…
The origin of biological motion can be traced back to the function of molecular motor proteins. Cytoplasmic dynein and kinesin transport organelles within our cells moving along a polymeric filament, the microtubule. The motion of the…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
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…
The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restricted to single-domain molecules, failing to address…
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins and widespread disruptions in brain function. Computational modeling has advanced our understanding of these processes, but efforts have traditionally…
The discoveries of numerous exciting phenomena in twisted bilayer graphene (TBG) are stimulating significant investigations on moir\'e structures that possess a tunable moir\'e potential. Optical response can provide insights into the…
The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-pieces-like particles, many other…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…