Related papers: Ordering in a fibrinogen layer
Spatially ordered systems confined to surfaces such as spheres exhibit interesting topological structures because of curvature induced frustration in orientational as well as translational order. The study of these structures is important…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
A simple molecular thermodynamic approach is applied to the study of the adsorption of gases of chain molecules on solid surfaces. We use a model based on the Statistical Associating Fluid Theory for Variable Range (SAFT-VR) potentials [A.…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
In periodically sheared suspensions there is a dynamical phase transition characterized by a critical strain amplitude $\gamma_c$ between an absorbing state where particle trajectories are reversible and an active state where trajectories…
Structural and mechanical differences between cancerous and healthy tissue give rise to variations in macroscopic properties such as visual appearance and elastic modulus that show promise as signatures for early cancer detection. Atomic…
Accurate quantification of protein-nanoparticle interactions is essential for applications in nanobiotechnology, nanomedicine, and drug delivery. Motivated by recent computational and experimental work, we combine coarse-grained united-atom…
Physisorption or chemisorption from dilute polymer solutions often entails irreversible polymer-surface bonding. We present a theory of the non-equilibrium layers which result. While the density profile and loop distribution are the same as…
Collagen is the most abundant extracellular-network-forming protein in animal biology and is important in both natural and artificial tissues, where it serves as a material of great mechanical versatility. This versatility arises from its…
Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse grained model, we systematically studied the folding and adsorption behavior of a…
Nanoscale molecular transport plays a crucial role in regulating mass diffusion and responsiveness in condensed matter systems. In soft porous crystals, in particular, adsorption of guest molecules induces host framework deformation and…
Improved performance in higher-order spectral density estimation is achieved using a general class of infinite-order kernels. These estimates are asymptotically less biased but with the same order of variance as compared to the classical…
Roughness and orientational order in thin films of anisotropic particles are investigated using kinetic Monte Carlo simulations on a cubic lattice. Anisotropic next-neighbor interactions between the lattice particles were chosen to mimic…
We present a new method for design problems wherein the goal is to maximize or specify the value of one or more properties of interest. For example, in protein design, one may wish to find the protein sequence that maximizes fluorescence.…
Amphiphilic molecules spontaneously form self-assembled structures of various shapes depending on their molecular structures, the temperature, and other physical conditions. The functionalities of these structures are dictated by their…
BAR superfamily proteins have a banana-shaped domain that causes the local bending of lipid membranes. We study as to how such a local anisotropic curvature induces effective interaction between proteins and changes the global shape of…
The determination of phase behavior and, in particular, the nature of phase transitions in two-dimensional systems is often clouded by finite size effects and by access to the appropriate thermodynamic regime. We address these issues using…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
We developed the models and algorithms to describe two main artefacts of AFM: (i) broadening effect and (ii) decreased heights of profiles for individual objects adsorbed on a hard substrate. It was shown how to measure elastic properties…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…