Related papers: Developing an unfolding-incorporated coarse-graine…
By mixing glass beads with a curable polymer we create a well-defined cohesive granular medium, held together by solidified, and hence elastic, capillary bridges. This material has a geometry similar to a wet packing of beads, but with an…
We study the mechanical stiffening behavior in two-dimensional (2D) cross-linked networks of semiflexible biopolymer filaments under simple shear. Filamental constituents immersed in a fluid undergo thermally excited bending motions.…
Blood clots occur in the human body when they are required to prevent bleeding. In pathological states such as diabetes and sickle cell disease, blood clots can also form undesirably due to hypercoagulable plasma conditions. With the…
Twisted bilayer graphene (TBG) develops large moir\'e patterns at small twist angles with flat energy bands hosting domes of superconductivity. The large system size and intricate band structure have however hampered investigations into the…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We study the conformations of polymer chains in a poor solvent, with and without bending rigidity, by means of a simple statistical mechanics model. This model can be exactly solved for chains of length up to N=55 using exact enumeration…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
Biopolymer gels, such as those made out of fibrin or collagen, are widely used in tissue engineering applications and biomedical research. Moreover, fibrin naturally assembles into gels in vivo during wound healing and thrombus formation.…
Soft matter systems are common in nature and make up nearly all the essential components necessary for life, from cells to the organelles within those cells. The ability of these soft materials to deform is crucial for the proper…
During the formation of a thrombus, the architecture of the growing platelet aggregate is heterogeneous, with areas of dense and loosely packed platelets. The surface of activated platelets facilitate biochemical coagulation reactions that…
Colloidal particles with mobile binding molecules constitute a powerful platform for probing the physics of self-assembly. Binding molecules are free to diffuse and rearrange on the surface, giving rise to spontaneous control over the…
Although thin films are typically manufactured in planar sheets or rolls, they are often forced into three-dimensional shapes, producing a plethora of structures across multiple length-scales. Existing theoretical approaches have made…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…
Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML…
Crumpling an ordinary thin sheet transforms it into a structure with unusual mechanical behaviors, such as enhanced rigidity, emission of crackling noise, slow relaxations, and memory retention. A central challenge in explaining these…
We report on a cellular pattern which spontaneously forms at the surface of a thin layer of a cohesive granular material submitted to in-plane stretching. We present a simple model in which the mechanism responsible of the instability is…
There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in…
Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems mesoscopic coarse-grained (CG)…