Related papers: Designing active colloidal folders
Colloidal gels are prime examples of functional materials exhibiting disordered, amorphous, yet meta-stable forms. They maintain stability through short-range attractive forces and their material properties are tunable by external forces.…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Active colloids and externally actuated semi-flexible filaments provide basic building blocks for designing autonomously motile micro-machines. Here, we show that a passive semi-flexible filament can be actuated and transported by attaching…
Active matter systems - such as a collection of active colloidal particles - operate far from equilibrium with complex inter-particle interactions that govern their collective dynamics. Predicting the collective dynamics of such systems may…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
Soft slender structures are ubiquitous in natural and artificial systems and can be observed at scales that range from the nanometric to the kilometric, from polymers to space tethers. We present a practical numerical approach to simulate…
The design of desired behaviors in mechanical metamaterials has produced remarkable advances but has generally neglected two aspects - the inevitable presence of undesired behaviors and the role of dynamics in avoiding such behaviors.…
Analysis of molecular scale interactions and chemical structure offers an enormous opportunity to tune material properties for targeted applications. However, designing materials from molecular scale is a grand challenge owing to the…
We consider a directed walk model of a homopolymer (in two dimensions) which is self-interacting and can undergo a collapse transition, subject to an applied tensile force. We review and interpret all the results already in the literature…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Active fluids generate spontaneous, often chaotic mesoscale flows. Harnessing these flows to drive embedded soft materials into structures with controlled length scales and lifetimes is a key challenge at the interface between the fields of…
Using numerical simulations, we characterized the behavior of an elastic membrane immersed in an active fluid. Our findings reveal a nontrivial folding and re-expansion of the membrane that is controlled by the interplay of its resistance…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
The design of complex materials and the formation of specific patterns often arise from the properties of the individual building blocks. In this respect, colloidal systems offer a unique opportunity because nowadays they can be synthesized…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…