Related papers: Anomalous proteinaceous shells with octagonal loca…
Surfaces in i-Al68Pd23Mn9 as observed with STM and LEED experiments show atomic terraces in a Fibonacci spacing. We analyze them in a bulk tiling model due to Elser which incorporates many experimental data. The model has dodecahedral…
The dodecagonal quasicrystal classified into the five-dimensional space group P126/mmc, recently discovered in a Mn-Cr-Ni-Si alloy, has been analyzed using atomic-resolution spherical aberration-corrected electron microscopy, i.e.…
A systematic study of 2-quasiparticle bands of the proton-rich odd-odd nuclei in the mass A ~ 70-80 region is performed using the projected shell model approach. The study includes Br-, Rb-, and Y-isotopes with N = Z+2, and Z+4. We describe…
Spherical nanoclusters and nanoparticles are rising materials whose functional design provides many useful applications ranging from catalysis, molecular sensing, gas storage to drug targeting and delivery. Here, we develop phenomenological…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
Amorphous solids appear to react elastically to small external strains, but in contrast to ideal elastic media, plastic responses abound immediately, at any value of the strain. Such plastic responses are quasi-localized in nature, with the…
We investigate experimentally and numerically the defect configurations emerging when a cholesteric liquid crystal is confined to a spherical shell. We uncover a rich scenario of defect configurations, some of them non-existent in nematic…
Quasicrystals are aperiodically ordered solids that exhibit long-range order without translational periodicity, bridging the gap between crystalline and amorphous materials. Due to their lack of translational periodicity, information on…
Recent studies reveal that certain viruses package a portion of their genome in a manner that mirrors the icosahedral symmetry of the protein container, or capsid. Graph theoretical constraints forbid exact realization of icosahedral…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
We present a new numerical scheme to study systems of non-convex, irregular, and punctured particles in an efficient manner. We employ this method to analyze regular packings of odd-shaped bodies, not only from a nanoparticle but also both…
Our understanding of physical properties of quasicrystals owes a great deal to studies of tight-binding models constructed on quasiperiodic tilings. Among the large number of possible quasiperiodic structures, two dimensional tilings are of…
Expanding the library of self-assembled superstructures provides insight into the behavior of atomic crystals and supports the development of materials with mesoscale order. Here we build upon recent findings of soft matter quasicrystals…
We describe optimized parallel tempering simulations of the 46-residue B-fragment of protein A. Native-like configurations with a root-mean-square deviation of approximately 3A to the experimentally determined structure (Protein Data Bank…
The majority of viruses are organised according to the structural blueprints of the seminal Caspar-Klug theory. However, there are a number of notable exceptions to this geometric design principle. Prominent examples are the cancer-causing…
We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…
In a recent Letter we proposed a means to realize a quasicrystal with eight-fold symmetry by trapping particles in an optical potential created by four lasers. The quasicrystals obtained in this way, which are closely related to the…
Lattice models have been used extensively over the past thirty years to examine the principles of protein folding and design. These models can be used to determine the conformation of the lowest energy fold out of a large number of possible…
Quantum anomalous Hall insulator/superconductor heterostructures emerged as a competitive platform to realize topological superconductors with chiral Majorana edge states as shown in recent experiments [He et al. Science {\bf 357}, 294…
Dense packings have served as useful models of the structure of liquid, glassy and crystal states of matter, granular media, heterogeneous materials, and biological systems. Probing the symmetries and other mathematical properties of the…